Latest improvements for QIAGEN CLC Main Workbench

Bug fixes

• Fixed an issue with the side panel settings where the label coloring of some restriction sites would always be black and the sorting would not be alphabetical when saved view settings were applied to a sequence.
• Fixed an issue in Maximum Likelihood Phylogeny that in rare situations led to tree construction never completing.
• Fixed an issue with Create BLAST Database, which could fail if the underlying native BLAST tool reported warnings.
• Improvements have been made to make it less likely that a “CPU usage limit was exceeded” error will be returned when running blastp, blastx, tblastn or tblastx using BLAST at NCBI.
• Fixed an issue affecting the naming of workflow outputs defined using a naming pattern of the form {input:N} or its equivalent {2:N}, e.g. {input:1} or {2:1}. The intended input name may not have been the one used to form the output element names when the workflow included an Iterate element, and the batch units were folders, defined based on the organization of the input data, and import was done on the fly.
• An element’s position within a folder in the Navigation Area can be controlled when copy/pasting, with the pasted element appearing above a selected element in the same folder. This fixes an issue introduced in CLC Main Workbench 8.1, where pasted elements were always placed at the bottom of the list in a folder when pasting.

Improvements

• GO Annotation File (GAF) 2.2 files can now be imported.
• Create Expression Clone (LR) output names include the Destination vector name first followed by the Entry clone name. Previously the naming pattern was inconsistent.

Bug fixes

• Right click menu options relating to exporting graph views that were missing in earlier CLC Main Workbench releases in the 21.x release line have been restored. This includes the “Open Graph in New View” and “Export Graph to Comma-separated File” options.
• Server import/export locations can again be pre-configured as export destinations in workflow export elements when logged into a CLC Genomics Server. This functionality was present in earlier release lines, but was not present in earlier 21.x versions.
• Fixed an issue where editing the reverse strand of a DNA sequence could result in extra bases being inserted.
• Fixed an issue in Extract Consensus Sequence so that insertions are no longer added in low-coverage regions.
• Fixed an issue affecting the graphical display of BLAST results, where HSPs matching the start of a subject sequence were shown as matching the entire sequence. This affected only the graphical overview. Information in the HSP table was correct.

Advanced notice

• Right-click functionality for launching installed, multi-input workflows in Batch mode will be retired in a future release of the software.

Bug fixes

• Fixed an issue that caused Download Blast Databases to occasionally fail when downloading a subset of databases from NCBI.
• Fixed an issue where deleting a portion of a sequence could cause an error to be reported.
• Fixed an issue where an error was produced when working with outputs of Design Primers when options in the side panel under Primer info were selected. The error appeared when the mouse cursor was subsequently moved over the sequence.
• Fixed an issue where an error resulted when trying to do the following actions when working with sequences in sequence lists: Insert Restriction Site Before/After Selection, Digest All and Create Restriction Map, Show Enzymes Cutting Inside/Outside Selection.
• Fixed an issue that caused an occasional error to arise when deleting bases in a circular sequence that also have restriction sites.
• Fixed an issue affecting Cloning Editor where switching between linear and circular sequence representations could cause the editor to report an error.
• Fixed an issue where Cloning Editor occasionally reported an error when running in Viewing Mode.
• Fixed issues present when working with Sanger assemblies when the “Lock top sequence” viewing option was enabled. Issues included not being able to scale the trace data, problems selecting bases in the sequences, and the right-click menu not offering the expected options.
• Fixed an issue where dragging the edge of contigs in Sanger assemblies beyond the viewing area caused the horizontal scroll bar to keep scrolling.
• Fixed an issue affecting Batch Rename, where if the term to be replaced in element names was not present, the names were deleted.
• Fixed an issue affecting naming patterns in export tools, and in workflow output and export elements, where upper case text within curly brackets in these patterns was translated to lower case when naming the outputs.
• Fixed an issue affecting workflows containing Iterate elements connected to more than one downstream element, where the batch overview step in the launch wizard to displayed the same input objects multiple times. This was a problem in presentation only. It did not affect the analyses.
• Fixed an issue affecting workflows containing Iterate elements when the names of input data element contained characters considered special by the operating system (e.g. on Windows : < > | ). When affected by this issue, no outputs would be produced or just a Workflow Result Metadata table would be produced.
• Fixed an issue affecting the Table view of long Sequence Lists, where the contents of the ‘Linear’ column could be missing for some sequences.
• Fixed an issue where table export of a Venn diagram did not export all the columns selected in the wizard.
• Fixed an issue affecting metadata tables where the paths to data elements that had been moved were not updated to reflect the new location.
• Various minor bugfixes

Plugin notes

Changes have been made that improve the speed of jobs on the CLC Genomics Cloud Engine (GCE) that involve large CLC data elements. This improvement affects systems where the Cloud Plugin is installed and Cloud Connection settings have been configured.

There are no changes to QIAGEN CLC Main Workbench 21.0.3 relative to version 21.0.2. Version 21.0.3 has been released as the corresponding client version for QIAGEN CLC Genomics Server 21.0.3.

Improvements and bug fixes

• Fixed an issue that prevented the use of saved view settings that included additional restriction enzymes (configured via the side panel settings). This issue could cause an error message to arise when the saved view settings were applied directly to an open sequence or sequence list, or when such view settings were applied generally for sequences in the Workbench Preferences.
• Fixed an issue where changes to the list of motifs, made via the side panel settings of sequences, were not saved when that view setting was saved.
• Fixed an issue where where the axis on a log plot could show the wrong value when zoomed out to the point where there were multiple orders of magnitudes between the indicators.
• Various minor improvements

Bug fixes

• Fixed an issue introduced in CLC Main Workbench 21.0, where stand-alone read mappings could not be opened.
• The Java version bundled with CLC Main Workbench 21.0.1 is Java 11.0.6, where we use the JRE from AdoptOpenJDK. This addresses an issue present in Java 11.0.8, included with CLC Main Workbench 21.0, which could cause Java applications on mac systems to crash when switching keyboard layouts.

Please see the release notes for CLC Main Workbench 21.0, below, for a full list of changes since the last general release of this software.

New features and improvements

Full workflow support for Sanger sequence analysis

New features have been introduced, and improvements made, to support automated analyses of Sanger trace data using workflows.

Trim Sequences

• Trim Sequences can now be used in workflows.
• Trim Sequences can be run on the CLC Genomics Server.
• A new sequence element containing the trimmed sequences is output. Previously, the input was modified and saved.
• A report can be generated containing a summary of the number of reads trimmed and the reasons for the trimming.
• The UniVec database used in this tool has been updated to version 10.0 of UniVec_Core.

Extract Consensus Sequence

• The Extract Consensus Sequence tool has been added to the Toolbox in the “Sanger Sequencing Analysis” folder.

Other improvements supporting trace data analysis in workflows

• Trace data can be imported using on-the-fly import in workflows.
• Improved output naming by the Assemble Sequences to Reference and Assemble Sequences tools: The sample name is included in the file name and the sequence names in the output.
• Metadata-based naming is supported in workflows run in batch mode or with Iterate control flow elements through the use of new placeholders: {metadata} and {metadata:<columnname>}.
• The Secondary Peak Calling tool no longer modifies the input data element, but instead produces new elements as output. Note: This change requires that the workflows with this tool that were created in older versions of the software must be manually updated. The old workflow element must be replaced by a new one. The recommended upgrade path for installed workflows containing the Secondary Peak Calling tool is to save a copy of the workflow in the Navigation Area using a version CLC Main Workbench 20.x, and then open and manually update that workflow in CLC Main Workbench 21.0. The new workflow can then be installed, if desired.

Combine Reports

The Combine Reports tool summarizes information from multiple reports and produces a single report. Previously this tool was only available in the CLC Genomics Workbench.

Workflow related

• When a workflow with Export elements is run in batch mode, the exported files from each batch run can be saved to separate folders.
• On-the-fly import can be used without metadata when running workflows in batch mode, and when running workflows containing a single Iterate element.
• Name placeholders for output elements and export elements have been updated, and the naming of outputs of workflows run in batch mode can be more finely controlled.
• Improvements for Workflow Input elements:
  • Workflow Input elements can be configured to limit the data input method to either selection of data elements from the Navigation Area or selection of files to be imported using on-the-fly import. The default is to allow the input method to be chosen when launching the workflow.
  • Workflow Input elements can be configured to limit the on-the-fly import types available when launching the workflow. Parameters of selected importers can also be locked or unlocked, as desired, defining whether the setting is configurable when launching the workflow.
• Additional configuration options for Iterate and Collect and Distribute workflow elements are available.
• When a workflow with Iterate elements is run with the “Batch” checkbox checked, the “Batch identifier” column in the Workflow Result Metadata table will contain the combined batch identifier, reflecting all levels of batching and iterations.

Performance improvements

• Improved the performance of the alignment editor for large alignments.
• Create Tree is significantly faster when creating large trees when using the Jukes-Cantor distance measure.
• Fixed an issue that could cause the CLC Workbench to become unresponsive when exporting large binding site tables generated by Find Binding Sites and Create Fragments.
• Improved the performance of searching for data elements associated with a metadata table when using the “Find Associated Data” button.
• Fixed an error that occurred when displaying very large trees.
• Performance has been improved when tools generating a large number of sequences (for example, Trim Reads) are run on a system with many threads.

Working with tables

• Column order can be adjusted when viewing tables, and the revised column order will be respected when exporting the open table to, for example, csv or excel format files.
• Tables in reports can be opened in a new tab: right click -> Open Table.
• Tables can be exported using a right-click option: “File” -> “Export Table”. The export takes into account filtering, ordering and deselection of columns.

Export

• Exported files can be saved into subfolders of the selected output area by using a forward slash character / at the start of the custom file name definition.
• Graphics export of Sequences, Alignments and Read mappings is supported as a standard export, which can be embedded into workflows and executed on a CLC Genomics Server. This feature is intended for high-throughput applications. For other applications, we recommend the existing graphic export tool.

Create Protein Report

Updates have been made relating to the BLAST functionality in Create Protein Report:

• The default expect value (e-value) for BLAST searches at the NCBI is 0.05, aligning with the defaults used at the NCBI.
• The top 10 BLAST alignments are included in the report, where previously it was the top 100. The full BLAST report continues to be available by clicking on the results in the report, and the full BLAST hit table continues to be included in the report.
• Results of searches against local sequences or databases can no longer be included in the report. (The standard BLAST tool remains available for running local searches.)

Improvements relating to connections to a CLC Server

• The CLC Server connection dialog will present information like the version and port of the selected CLC Server prior to login, when that information is available.
• The CLC Server connection dialog will close automatically after the “Log In” button is clicked. The login process runs in the background, indicated by a flashing server icon in the lower left corner of the Workbench.
• When the Workbench loses connection to a CLC Server, it attempts to reestablish the connection. Open views of data stored on the CLC Server are not closed.
• When selecting files stored on a CLC Server, only files with the relevant extensions are listed, together with their date of last modification and the size of the files.

Other improvements

• Stand-alone Read Mapping, Contig and BLAST Graphics views support wrapped sequence layouts. The relevant option is available in the side panel. This may be of particular interest when working with Sanger trace data.
• Import Metadata uses the name of the imported spreadsheet when naming the resulting metadata table.
• The element History view has been updated, and its performance has been improved when handling many history entries.
• Improved the rendering of annotations in the Export Graphics tool when used with the “Export whole area” option.
• When hovering the mouse cursor over a Sequence List in the Navigation Area, the tooltip includes information about the sequencing platform, if this information is available.
• The log can be saved as part of the output when running a tool or workflow in the Workbench.
• Data locations can be added when using the Workbench in Viewing Mode.
• Custom attributes can be configured in a data location such that attribute values are not copied when copying data elements.

Bug fixes

• Fixed an issue affecting annotations of restriction sites for enzymes cutting within the recognition site, where the arms indicating the cut site spanned large sequence regions, instead of indicating the cut site.
• Fixed an issue where the Search for Sequences at NCBI tool would occasionally return fewer rows than configured in the ‘Number of hits’ preference setting.
• Fixed an issue where “Reset tree topology” in the phylogenetic tree editor could fail in some cases when input sequences were extracted from (at least) two different trees.
• Fixed an issue where external files could not be opened on Windows Server 2019.
• Fixed an issue where the Ctrl+F keyboard shortcut did not activate the ‘Find’ side panel when viewing a track list.
• – Fixed an issue where, on Mac OS, clicking CLC URLs (“clc://…”) would open an older version of the Workbench even after installing a new version.
  – The list of file types automatically associated with the Workbench has been updated to only include CLC files (xxx.clc). On Mac OS only, the Workbenches would previously be associated with the set of file types that can be imported using the ‘Standard Import’ tool. The Workbench can still be associated to any given file type using the standard tools of the operating system in question.
• Fixed an issue where a path specified in the path.properties configuration file was not properly interpreted if it was specified in ‘Windows syntax’, e.g. “x:\myDrive\temp”
• Fixed an issue in Excel importer, where the presence of certain formulas would previously prevent successful import.
• Fixed an issue where, if BLAST at NCBI failed with an error, no error would be shown and instead no hits were returned.
• Fixed an issue where some workflows using a Collect and Distribute element with multiple output channels did not pass the correct inputs to a tool after the Collect and Distribute element.
• Fixed an issue where compressed data elements sometimes appeared to have “Compression enabled: No” in the Element Info tab.
• Fixed an issue in the Navigation Area that caused move operations to be converted to copy operations if the Navigation Area was refreshed before the move was completed.
• Various minor bug fixes

Changes

• The Java version bundled with CLC Main Workbench 21.0 is Java 11.08, where we use the JRE from AdoptOpenJDK.
• The default base name for the element being exported is designated using the placeholder {name}, instead of {input}. The numeric equivalent, {1}, is unchanged. The default export naming pattern has correspondingly been changed to {name}.{extension}. (GxS notes only, add the following: This change also applies to exports configured in External Applications.) Previously {input} was used.
• The default expect value (e-value) for BLAST at NCBI is 0.05 and the maximum number of hits is 5000, aligning with the defaults used at the NCBI.
• Changes have been made to the handling of sequence identifiers when using Create BLAST Database. This change allows continued flexibility in the naming of sequences used for making these databases, avoiding direct exposure to limitations present in the underlying BLAST+ program, makeblastdb, such as not allowing long or duplicate sequence names. Further details are provided in our FAQ area.

Functionality retirement

Tools

• Reverse Sequence

Improvements and Changes

• The maximum number of hits returned by BLAST at NCBI is now 5000, aligning with the defaults used at the NCBI.
• Various minor improvements

Bug fixes

• Fixed an issue affecting annotations of restriction sites for enzymes cutting within the recognition site, where the arms indicating the cut site spanned large sequence regions, instead of indicating the cut site.
• Fixed an issue that could cause the CLC Workbench to become unresponsive when exporting large binding sites tables generated by the Find Binding Sites and Create Fragments tool.
• Fixed an issue where, if BLAST at NCBI failed with an error, no error would be shown and instead no hits were returned.
• Fixed a bug where some workflows using a Collect and Distribute element with multiple output channels did not pass the correct inputs to a tool after the Collect and Distribute element.

Improvements

• The NCBI nucleotide database “Betacoronavirus”, focused on SARS-CoV-2, has been added to BLAST at NCBI.
• Names of extracted consensus sequences now have the pattern: “<input name> <reference name> consensus”.
  
• The vertical range when viewing chromatograms has been increased, allowing the full view of all peaks, even in noisy data containing many small peaks.

Bug fixes

• Fixed an issue where options of Extract Annotations were not configurable in workflows.
• Fixed an issue where unnecessary, empty output folders could be generated by analyses run in batch mode. This happened when the “Create subfolders per batch unit” option was enabled, and the “Include” or “Exclude” field had been used to specify elements within each batch unit to analyze, such that some batch units were empty.
• Fixed an issue where the Standard Importer for Fasta Alignments would fail when importing multiple files.
• Fixed an issue where importing a Clone Manager file (.cm5) where a sequence length annotation would be ignored and the full sequence imported.
• Various minor bugfixes

Advanced notice

• The Reverse Sequence (legacy) will be removed in a future version of the software.
• The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the “Batch” checkbox when selecting input data.

If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Bug fixes

• Fixed an issue with Create BLAST Database, where BLAST databases could not be created if the sequence set included entries with identifiers longer than 50 characters or of a form similar to PDB identifiers. This was due to new requirements introduced with NCBI BLAST+ 2.8.1. To address this, we have replaced the BLAST+ 2.9.0 makeblastdb tool, used by Create BLAST Database, with the version from BLAST+ 2.6.0. This is the same version used in CLC Main Workbench 8.1.x. This change does not affect the searching of BLAST databases using this or earlier supported versions.
• Fixed an issue affecting the Search for Sequences in Uniprot tool where sequences could not be downloaded due to changes to the Uniprot database format. Uniprot entries downloaded now may have small differences in the content of some fields relative to downloads made in the past.
• Fixed an issue that sometimes prevented the selection of individual data elements as inputs to a workflow, allowing only folders to be specified, when the “Batch” box was checked.
• Fixed an issue where the output naming pattern of a workflow was not properly respected if output channels of one or more elements were connected to both a Collect and Distribute element and to an Output element.
• Fixed an issue that prevented printing to certain types of printers on Windows 10 systems.
• Fixed an issue that could prevent the export of graphics in PDF format, if an older version of the software had previously been used to export graphics.
• Fixed an issue where sequence annotations were sometimes incorrectly rendered at some zoom levels for sequences, sequence lists and whole genome alignments.
• Fixed an issue that could cause scrolling through data in an open tab to continue for some time when a selection in an editor was dragged to somewhere outside the editor and the mouse button then released.

Advanced notice

• Reverse Sequence (legacy) will be removed in a future release of the software.
• The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the “Batch” checkbox when selecting input data.

If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• Metadata associations are preserved when importing .zip files containing both metadata tables and associated data.
• Various minor improvements

Bug fixes

• Fixed an issue where data elements selected in the Navigation Area were sometimes incorrectly preselected when browsing for inputs in wizard steps of tools and workflows.
• Fixed a bug that prevented installed workflows with configuration options and at least one locked input from being configured through the Workflow Manager
• Fixed an issue where some plots, including volcano plots and scatter plots, sometimes showed an incorrect tooltip when hovering over a data point with the mouse.
• Fixed an issue when workflows were run in the batch mode or using Iterate elements, where if two input elements with the same name but in different folders were selected from the Navigation Area, and the “Use organisation of input data” option was chosen, then the inputs were allocated to the same batch, even though the batch overview showed that they would be in different batches. Now, they will be allocated to different batches, as shown in the batch overview.

General information

NCBI plans to change their blast database folder structure in early February 2020. When that happens, the Download BLAST Databases tool of QIAGEN CLC Main Workbench 20.0.2, and future updates, will list the new, dbV5 blast databases for download. The Create Blast Database tool will continue to create dbV4 databases. Databases of either version can be searched using the blast programs included in QIAGEN CLC Genomics Main 20.x release line.

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software.
The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the “Batch” checkbox when selecting input data.

If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• Import of Gene Ontology Annotation files now supports files including BOM encoding.
• The hmmsearch program, used by Pfam Domain Search, is now 64-bit on all platforms. Previously a 32-bit version was distributed for use on macOS.
• File information is now included when printing the data from the Element info view.

Bug fixes

• Fixed a bug in the Primer Designer, where clicking on each potential primer starting position did not highlight the the primer region.
• Fixed a bug where sequences could not be downloaded from NCBI through the ‘Show BLAST Hit Table‘ view
• Fixed a bug in the advanced filter of the table view of sequence lists, where days and months could not be matched with corresponding values in the “Modified” column.
• Fixed a bug in Experiments where very long column group headers could cause an “out of memory” error on macOS.
• Fixed an issue in the element history of a result generated by Extract Annotations, where the reference sequence track could appear to have been used for extracting annotations, even when it was not used.
• Fixed a bug in workflows using control flow elements, where some outputs were not saved if the same output channel was connected directly to both an output element and to a Collect and Distribute element. This problem occurred if the combined lengths of the input filenames for a given run exceeded 250 characters, and batch units were defined on the basis of the organization of the input data.
• Fixed a bug in workflows containing two Iterate elements connected to each other, where it was not possible to select a metadata column for the inner Iterate element in the batch configuration step of the workflow wizard if two or more connections were made from the output channel of that element.
• Various minor bugfixes

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software.
The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the “Batch” checkbox when selecting input data.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

New features

Protein structure and homology

• Generate Biomolecule A new tool available from the side panel of Molecule Projects allowing biomolecules to be generated or extracted based on symmetry information in PDB files.
• Find and Model Structure A new tool that finds suitable protein structures for representing a given protein sequence. From the resulting table, a structure model (homology model) of the sequence can be created by one click using one of the found protein structures as template.
• Download 3D Protein Structure Database A new tool for downloading a curated database containing sequences with known 3D structures obtained from the Protein Data Bank
• Molecule structures in a Molecule Project can now be exported to a PDB format file.
• Search for PDB Structures at NCBI is now available when running the Workbench in Viewing Mode.

Workflows

• When launching workflows, batch units can now be defined using metadata, supplied either as a CLC medata table or by selecting an Excel format file containing information about the data.
• Workflows with multiple inputs, where those inputs should be matched with each other, can now be launched in batch mode, making use of the ability to define batch units based on metadata. For example, a workflow where sets of reads should be mapped to different reference sequences can now be launched in batch mode.
• Two new workflow elements have been introduced, Iterate and Collect and Distribute, which allow workflows to be designed where the execution of different parts of a workflow can be finely controlled. For example, using these elements, a single workflow can contain an analysis step that will be run once per sample, as well as elements that should only be run once for a set of samples.
• Workflows now produce a Workflow Result Metadata table, which contain one row per output, with the relevant data element associated with that row. When launched in batch mode, the batch the row relates to is clearly indicated.
• CLC sequence files not yet imported can be imported on the fly, as an initial action when a workflow is run, avoiding the need import such data prior to launching the workflow. This is mostly of relevance if sharing data with other sites.

Export

• Reports can now be exported in PDF format.
• When exporting to PDF, there is now an option to export the history of the report.

BLAST

• A new option for the BLAST tool called Filter out redundant results, will when enabled cull HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP.
• The NCBI blast executables have been updated to version 2.9.0.
• The option “Choose filter to mask low complexity regions” has been renamed to “Mask low complexity regions”.

Improvements

Workflows

• All installed workflows can now be updated in a single operation from the Workflow Manager using the new Update All Workflows button.
• Placeholder-based naming of outputs in workflows can now be configured at a finer level: the {input} or {2} placeholder is now replaced by the name of the first workflow input by default. This can then be further configured to use the names of other inputs by specifying them by number after a colon in the placeholder. For example: {2:1,3} would be replaced by the names of workflow inputs number 1 and 3. Previously, a workflow output configured as {2} was replaced by a concatenation of all the workflow input names.
• The listing of items in the “Add Element” dialog in the Workflow Editor has been made improved. Installed workflows in the workbench, and no longer matches texts in the tooltips of the tools.
• When running a workflow configured to use reference data, the Reference Data Set selection step has been updated to show the list of preconfigured elements in the tooltip.
• The “Export to PDF” tool can now be used in workflows to export reports in PDF format.

Performance improvements:

• Saving analysis results to an SSD is now considerably faster.
• The import of ZIP files has been improved: temporary objects are cleaned up during the import process, reducing the required disk space.
• Moving and deleting many elements at once is now faster.
• Emptying the Recycle bin now takes place in the background.
• Messages from tools are no longer presented in the form of black bubbles in the Processes area. Messages are still writtent to the log.
• There are general performance improvements in the following areas:
  • The Navigation Area
  • BLAST and Add attB Sites tools when using large sequence lists
  • Opening large protein sequences
  • Making BLAST databases where most sequences have the same name.

Import and export

• When exporting to PDF, there is now an option to export the history of the report.
• The CSV importer has been updated:
  • Values no longer need to be enclosed in quotation marks in the CSV file to be successfully imported.
  • Data values starting with a numeric character but also containing non-numeric characters are now interpreted as text. Such values were previously converted to numbers and then only imported up to the first non-numeric character.
• The import of Nexus files has been updated to more closely match the format specifications.
• When selecting files to import from an import/export directory on a QIAGEN CLC Genomics Server, right-clicking on a folder name now brings up a menu with the options: “Add the content of a directory” or “Add the full content (recursively) of a directory”.
• The “Excel 2010” and “Excel 97-2007” exporters now export NaN and +/-Infinity values to #N/A.
• When importing multiple files using the Standard Import, the process ends with an error if at least one of the files failed to import. The details of which file failed and why can be seen in the log.
• The GenBank exporter now replaces any spaces in annotation names with underscores.

Searching

• It is now possible to search for values contained within metadata tables.
• Elements in the CLC_References locations can now be found by searches.
• Elements in a Recycle Bin can now be found by searches.

Metadata related

• Metadata tables can be moved to a new File Location while maintaining metadata associations.
• Three matching schemes are now available for associating data with metadata, based on matching data element names with values in the metadata key column: Exact, Prefix and Suffix. Suffix is a new option, where matches are sought starting from the end of data element names. Prefix, previously named Partial, looks for matches from the beginning of data element names. Exact, as in earlier versions, seeks exact matches between data element names and metadata key column values.

Create Box Plot

• Create Box Plot now calculates the median and percentile values in the same way as the “quantile” method in R.
• Whiskers of boxplots now range from the lowest data point within 1.5 times the inter quartile range (IQR) of the lower quartile and the highest data point within 1.5 IQR of the upper quartile. Previously, they extended 1.5 times the length of the box (IQR).

Other improvements

• Outputs of tools provided by plugins now include the plugin name and version in the element history.
• A new option when right-clicking on a table cell, Edit | Copy Cell, allows individual cells to be copied to the clipboard. Previously only whole rows could be copied
• Tool and workflow logs now display an “Elapsed time” column.
• In the tree view of phylogenetic trees, the “Reset Tree Toplogy” button will now also uncollapse any collapsed nodes.
• The name of a non-default workspace is now shown in the Workbench title bar.
• The table view (“Show Table”) of plots has been improved in the cases where multiple data series are shown in the plot. The table now includes all of the x values from all data series, instead of the x values from just the first data series. If a data series is missing a y value for a specific x value, than the entry in the table will be empty.
• The maximum size of a plot in a report displayed in the Workbench has been increased too 800 pixels, and the width/height ratio has been changed from 2/3 to 1/2.
• The ranking of search results in Quick Launch has been improved.
• CLC URLs have been made more compact.
• The icon for the sequence view has been changed for protein sequences, so it is possible to distinguish protein sequence views from nucleotide sequence views based on the icon.
• In the Reference Data Management dialog, the “usable free space” is shown instead of the previous “free space”.
• In the Batch Rename tool, the option ‘Replace part of the name’ fields have changed from ‘From’ and ‘To’ to ‘Replace’ and ‘With’ for clarification.

Bug fixes

• Fixed an issue affecting mac OS X setups with accessibility settings enabled, where the “Replace Selection with Sequence” functionality available from within the Cloning editor could fail with an error.
• Fixed a bug where workflow installer files did not include the specified icon.

Changes

• The Java version bundled with QIAGEN CLC Main Workbench 20.0 is Java 11, where we use the JRE from AdoptOpenJDK.
• Using Local Search, searches for sequences with a specific length or length range now only returns individual sequence elements that meet the search requirements. Previously searches were also done within other types of elements, e.g. sequences lists, read mappings, etc.
• The Help -> Tutorials menu item has been replaced with Help -> Online Tutorials, which opens the online tutorials in a browser.
• The Reverse Sequence tool has been moved to the Legacy folder of the Workbench Toolbox and “(legacy”) appended to its name. It will be removed in a future version of the software.

Plugin notes

New plugins

• Navigation Tools Provides the functionality formerly provided by the Bookmark Navigator and Recent Items Navigator plugins.
• SignalP and TMHMM Provides the functionality formerly provided by the SignalP and TMHMM plugins

Plugin retirements

The following plugins have been retired, with their functionality being provided by a new plugin:

• Bookmark Navigator
• Recent Items Navigator
• SignalP
• TMHMM

The following plugins have been retired and their functionality is no longer available through the QIAGEN CLC Main Workbench:

• PPfold
• TRANSFAC

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software. The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the “Batch” checkbox when selecting input data. If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• Download Blast Databases now retrieves databases from the dedicated version 4 archive (“v4” folder) at the NCBI. From February 4, 2020, this tool in older versions of the software retrieves version 5 (dbV5) blast databases, which cannot be searched using the BLAST search tool in this release line or earlier lines. (QIAGEN CLC Main Workbench 20.0 and higher can be used to download and search dbV5 blast databases.)
• The hmmsearch program, used by Pfam Domain Search, is now 64-bit on all platforms. Previously a 32-bit version was distributed for use on macOS.
• Various minor improvements

Bug fixes

• Fixed a bug where sequences could not be downloaded from NCBI through the ‘Show BLAST Hit Table‘ view.
• Fixed a bug in the Primer Designer, where clicking on each potential primer starting position did not highlight the the primer region.

Improvements

• Improved the stability and performance when using tools that communicate with the NCBI. This will provide noticeable improvements when retrieving large numbers of search results or downloading large numbers of sequences using tools like Search for Sequences at NCBI.
• Improved the placement of figures when reports are exported to PDF.
• Improved the stability of workflow execution when the data is placed on a Network File System (NFS).

Bug fixes

• Fixed an issue where a large nucleotide sequence could be detected as a protein sequence when being extracted from a BLAST database.

Advanced notice

The PPfold plugin will be retired  as of the next major release of the QIAGEN CLC Workbenches and Servers.
The TRANSFAC plugin will be retired as of the next major release of the QIAGEN CLC Workbenches and Servers.
If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Please also refer to the Latest Improvements listing for CLC Main Workbench 8.1.1 below to see all the changes that have taken place since CLC Main Workbench 8.1.

Bug fixes

• Fixed an issue where an error could occasionally arise during workflow validation when adding or connecting workflow elements in the workflow editor.
• Fixed an issue where the installation of large plugins occasionally failed.

Advanced notice

The PPfold plugin will be retired  as of the next major release of the CLC Workbenches and Servers.
The TRANSFAC plugin will be retired as of the next major release of the CLC Workbenches and Servers.
If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• In tracks/track lists, entering “chr4” or “4:” in the location field now searches for a chromosome named “4”, “chr4” or “chromosome_4”, instead of selecting the 4th chromosome in the drop-down menu.
• Columns in variant tables are now ordered more consistently.

Bug fixes

• The BLAST Selection Against NCBI and BLAST Selection against Local Data options are once again available in the right-click context menu for sequence selections in a sequence view.
• Fixed a bug where the Download BLAST Databases tool sometimes failed with an error during download.
• Fixed an issue where the table from Create Pairwise Comparison would not update correctly when the number of decimals to be shown was changed.
• Fixed an issue causing the Workbench to freeze when showing a heat map where all entries are identical.
• Fixed an issue where the PDF export of reports did not contain column headers if the first header was empty.
• Fixed an issue where text files did not have the expected “.txt” extension after a “Tab delimited text” export with the “Output as a single file” option selected.
• Fixed an issue where the Excel and PDF export of reports failed for reports that contained empty tables.
• Fixed an issue with the Search for Sequences at NCBI tool, where the search could fail when the Workbench had been configured to use a proxy server.
• Fixed a bug where numeric columns with at least five “?” would be left aligned instead of right aligned.
• Fixed a bug where, when launching a CLC Workbench using a CLC URL pointing to a data element stored on a CLC Server location, the data element was not opened automatically inside the Workbench after startup.
• Fixed an issue caused by a bug in Java 10 where files resulting from an analysis were occasionally corrupted. Often this affected analysis log files, but could affect other outputs. This affected GPFS file systems, and could affect other distributed file systems. CLC Main Workbench 8.1, and any versions released with the version 8.1.x, use Java 10. While we have worked around this issue so that analysis results files should no longer be affected by it, we recommend that the software itself not be installed directly on a GPFS file system.

Advanced notice

The PPfold plugin will be retired  as of the next major release of the CLC Workbenches and Servers.
The TRANSFAC plugin will be retired as of the next major release of the CLC Workbenches and Servers.
If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

New features

• A folder called Utility Tools has been introduced, which contains the tools Batch Rename and Extract Annotations tools. The folder under Molecular Biology Tools called Sequencing Data Analysis is now called Sanger Sequencing Analysis. The Toolbox | Workflows folder has been renamed Installed Workflows.
• The Batch Rename tool allows sets of data elements, or members of a data element (e.g. sequences in an alignment or reads within a read mapping) to be renamed. Changes can be simple, like adding text to the start or end of names, or more complex changes, using regular expressions or custom options. This tool was formerly delivered in the Batch Rename plugin, but is now integrated into the Workbench.
• An item called CLC Server Connection has been introduced under the File menu. This launches a dialog for connecting from the Workbench to a QIAGEN CLC Server. This functionality was formerly delivered in the QIAGEN CLC Workbench Client Plugin, but is now integrated into the Workbench.

Improvements

• Data created in QIAGEN CLC Main Workbench 8.1 will be internally compressed by default. Options are available for for exporting data without this compression or for disabling it entirely.
• A new option allows users to “Export table as currently shown” – including all filter settings and potential additional columns selected using the Side Panel.
• Tooltips on data elements in the Navigation Area show the following additional information: type of the element (e.g. Sequence List), file size, and compression status.
• It is now easier to reorder items in the Navigation Area. It was not previously possible to change the order of adjacent folders.
• Searching in the Navigation Area is now available when using the workbench in Viewing Mode.
• When starting the workbench with a “clc://” argument, the requested element is now selected in the Navigation Area.
• On macOS, the standard file browser is now used for browsing files. Previously, a third-party library was used.
• A new filtering button in all tables allows users to display in the table view only pre-selected rows.
• The ‘is in list’ table filter now supports tabs as a list separator. This makes it possible to paste rows from Excel into the search field.
• The Import tool allows for entering folder paths in the File name field.
• NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI.
• The Search for Sequences in UniProt tool is now available in Viewing Mode.
• The Search for Sequences in Uniprot tool has been updated to use the HTTPS protocol which is now required by UniProt.
• When using Search for Sequences at NCBI or Search for Sequences in UniProt to download sequences, the name of the searched database is now reported in the History view. If multiple sequences are downloaded, the resulting Sequence List now also has details in the History view.
• The Download BLAST Databases tool now requires less disk space when downloading and installing BLAST databases.
• The history information associated with results from the BLAST and BLAST at NCBI tools now includes the version of the BLAST software used for the search.
• When right-clicking a CDS annotation on a stand-alone sequence, the option “Translate CDS/ORF…” gives a choice between translating using a selected code translation table or by extracting the translation code from the annotation itself if this information is available.
• The Show History View no longer has a restriction on the number of elements shown.
• A message now warns if a bug report fails to reach Support using Help | Contact Support.
• The Create installer for workflows dialog has additional fields for specifying information about the workflow’s author.
• A “Check for updates” functionality is now available from the Help menu.
• Improved error message when attempting to save a file that is not the newest copy.
• The tool called Replace Selection With Sequence which appears in context menus for sequences in the cloning tool will now be disabled when the sequence is linear but a selection spanning the end to start position has been made. Reasons why sequences cannot be marked as circular or linear are now described more clearly in the tooltip.
• The format of the serverinfo.properties file has been changed. The new format supports up to 8 servers.
• The “Whole Genome shotgun-reads (wgs)” database has been removed from the BLAST at NCBI tool. Growth in the database means that specialized variants of BLAST are now required for search. More details on these can be found here.
• Track lists now display additional information about an annotation when hovering on it with the mouse cursor: the name and strand of the annotation, which exon is currently being hovered over and the position of the mouse cursor relative to the start of the annotation. This information is available in the ruler shown in the reference track of a track list, as well as in the lower right corner of the workbench.
• Sequence annotations where the strand is not known are now drawn without an arrow to distinguish them from annotations on the plus strand.
• The Reverse Sequence tool now names the output sequence name with the input sequence name followed by “-R” .
• Various minor improvements.

Bug fixes

• Fixed a problem introduced in QIAGEN CLC Main Workbench 8.0 where launching a tool from the Quick Launch window after sorting led to the wrong tool being started.
• Fixed an issue where the Motif Search tool would incorrectly update the input file.
• Fixed an issue where it was possible to create an empty alignment editor, causing the Workbench to crash.
• Fixed bug that caused import of empty text files to stall.
• Fixed an issue found in the History of a result generated by the Extract Annotations tool, that would incorrectly show that a reference sequence track was used when it was not.
• Fixed the links to the AmiGO Gene Ontology website used for GO annotations.
• Fixed the links to the HGNC (HUGO Genome Nomenclature Consortium).
• On Windows 10 and Windows Server 2016, the default BLAST database location will now be either ‘C:\Users\USERNAME\My Documents\CLCdatabases’ or ‘C:\Users\USERNAME\Documents\CLCdatabases’. Previously it was ‘C:\Users\USERNAME\CLCdatabases’.  When upgrading from earlier versions, an existing BLAST database location will not be modified and will continue to work.
• On some Windows 10 and Windows Server 2016 systems, the log files, user settings file, and workflow files, normally stored in ‘C:\Users\USERNAME\AppData\Roaming\CLC bio\Workbench’ were installed in ‘C:\Users\USERNAME\Application Data\CLC bio\Workbench’. Now we instead store these files in ‘%APPDATA%\CLC bio\Workbench’. User settings and workflow files will be automatically copied to the new location if they were previously stored in ‘C:\Users\USERNAME\Application Data\CLC bio\Workbench’.

Plugin notes

Plugin retirements

• QIAGEN CLC Workbench Client Plugin The CLC Server Connection item under the File menu has replaced the need for this plugin.
• Batch Rename  The Batch Rename tool, formerly delivered by this plugin, is now available directly in the Workbench under the Utility Tools folder.

Advanced notice

The PPfold plugin will be retired as of the next major release of the QIAGEN CLC Workbenches and Servers.
The TRANSFAC plugin will be retired as of the next major release of the QIAGEN CLC Workbenches and Servers.
If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Improvements

• NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI
• The Search for Sequences in Uniprot tool now uses the HTTPS protocol.

Bug fixes

• Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again.
• Fixed the links to the AmiGO Gene Ontology website used for GO annotations.

Notice

Only 64 bit versions of the QIAGEN CLC Main Workbench are available for QIAGEN CLC Main Workbench 8.1, released November 28, 2018, and above.

Bug fixes

• Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
• Fixed an issue with the advanced table filter functionality that prevented the removal of empty entries from columns expected to contain text.
• Fixed an issue where Excel formatted files (.xls, .xlsx) could not be imported as Trim Adapter Lists.
• Fixed a license issue causing workbenches to not start properly on Turkish Operating Systems.
• Fixed issue causing the license assistant dialog and EULA dialog to be too big for smaller screens.
• Fixed an issue where weblinks to Uniprot sequences led to the homepage.

Advanced notice

With a release planned for late 2018, only 64 bit versions of the QIAGEN CLC Main Workbench will be made available. 32 bit versions will be discontinued from that time.
If you are concerned about this change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).

Improvements and new features

• Workbenches without a license can now be run in Viewing Mode. In this mode, data can be viewed, imported and exported. Plugins needed for viewing certain data types can be installed. Viewing mode, with its added functionalities, replaces Limited Mode.
• A dialog is now presented on startup if there are installed workflows that need to be updated before they can be run. The information about what to do to when a workflow needs to be updated has been improved.
• The history of a data element can now be exported as a CSV format file.
• Changed amino acids colors to better suit users with various forms of color blindness.
• The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of QIAGEN CLC Main Workbench, so the version available for download could change over time from the one recorded here.
• In table views, it is now possible to filter columns with the filters “Is in list” and “Is not in list” when the values are numbers.
• Importing a GO annotation file with the Standard Import tool, specifying the format “Generic annotation file for expression data”, now fails with an informative warning if any of the GO annotations are truncated.
• Warnings are now reported if truncated GO annotations are found when opening data created by the Create Expression Browser tool.
• The ‘Expression Browser Table’ (output from the Create Expression Browser tool) now preserves sorting when changing the grouping, if sorting is not on any of the grouped columns.
• All wizard steps are now shown in the wizard sidebar when starting a tool or workflow.
• Visualization of features that wrap around the origin of circular sequences has been improved for sequences.
• Table filtering and search now interpret thousands and decimal separators in the same manner as the displayed table. Previously US punctuation was always used. This change means that if a table displays numbers in the form “123.456,7” then it is possible to find numbers less than ten by searching for “< 10,0” or “<10”, but not “<10.0”. If the table displays numbers in the form “123,456.7” then it is possible to find numbers less than ten by searching for “<10.0” and “<10”, but not “<10,0”.
• When a tool is disabled in a right-click context menu, hovering the mouse over the tool name will now reveal why a tool was disabled in most cases.
• The help window can now be closed by pressing the escape key.
• HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
• A warning message is now presented when the tool Extract Sequences is run with the “Extract to single sequences option” selected and more than 100 sequences would result.

Changes

• The Search for Sequences at NCBI tool now uses accession.version identifiers instead of GI numbers, as GI numbers are being phased out by NCBI (see https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/. )
• Scrolling in a table now scrolls a fixed number of pixels, and not a fixed number of rows or columns.
• The “Help” and “Reset” buttons in pop-up dialogs are now buttons with text labels. They were previously buttons with icons.
• The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
• Upgraded NCBI blast executables to version 2.6.0 for 64-bit systems. 32-bit systems still use version 2.2.30.

Bug fixes

• Fixed an issue where filtering a log for a job that was still running would result in error dialogs.
• Fixed an issue that had previously prevented configuration of the export option “Output as single file” in workflows.
• Fixed an issue where data exported with gzip or zip compression did not have the .gz or .zip suffix appended to the filename when earlier exports had been made with the same name and export location specified.
• Fixed an issue that could cause exports of reports with line graphs to fail.
• Fixed a bug where a cell containing multiple hyperlinked URLs caused export to Excel 2010 or Excel 97-2007 format to fail. Such cell contents are now written in plain text.

Plugin Notes

• Licenses for commercial modules are no longer required to install a module on a Workbench nor to view data generated by tools of a commercial module.
• The flexibility associated with network module licenses has been improved. Workbench module licenses provided via a CLC License Server are now initially loaded only when a tool provided by that module is launched. Such licenses are returned when 4 hours lapses since the last module tool was launched from that Workbench.

Advanced Notice

With a release planned for late 2018, only 64 bit versions of the QIAGEN CLC Main Workbench will be made available. 32 bit versions will be discontinued from that time.

Improvements

• NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI.
• The Search for Sequences in Uniprot tool now uses the HTTPS protocol.
• Fixed the links to the AmiGO Gene Ontology website used for GO annotations.

Bug fixes

• Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again.
• Weblinks to UniProt sequences are now working again.
• Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.

Advanced notice

Only 64 bit versions of the QIAGEN CLC Main Workbench are available for QIAGEN CLC Main Workbench 8.1, released November 28, 2018, and above.

• Improved the information about what to do to when a workflow needs to be updated.
• Various minor bugfix.

Bug fixes

• Fixed an issue with the Cloning tool introduced in the QIAGEN CLC Main Workbench 7.9 where the tool could not be launched.

New features

• Added keyboard shortcuts to change editor views. Ctrl + Shift + PageUp and Ctrl + Shift + PageDown now changes the current view of the currently focused editor.
• New keyboard shortcuts are available for navigation within the workbench:
  • Navigate between open tabs with Ctrl + Page Down and Ctrl + Page Up (Windows/Linux/Mac). On laptops without Page Up/Down keys, the shortcuts are Ctrl+fn+arrow up/down.
  • Return focus to the navigation area with Alt + Home.
• We have made the following improvements to tab presentation in the View area of the Workbench:
  • Tabs show more of the name of the opened object.
  • Tabs now open from the top left corner to the right and down.
  • Tabs always stay in the same position when another tab is selected or a new tab is opened.
  • A new sub menu has been added to the right click menu on tabs to select between the open tabs.
• Anonymous Workbench usage information can now be shared with us to help us improve our products and offerings. Information about what is collected and how to opt out is provided when the updated Workbench is launched. Further details areavailable in the manual.

Improvements

• New and improved Save View Settings dialog. This new dialog can be used for saving, applying, importing and exporting side panel views.
• Opening large pairwise comparisons generated by the the Create Pairwise Comparison tool is now faster.

Bug fixes

• Fixed an issue where the GFF3 Exporter could generate invalid GFF3 for features of length 0.
• Fixed a rare issue that could cause GenBank export to fail.
• Fixed an issue with the Realign Selection tool where clicking on the ? button to see the manual information resulted in an error. This tool is launched from the right-click context menu for selections in sequence alignments.
• Fixed an issue where workflows run in batch mode would fail in the case where no results are saved to the Navigation Area and only one file is exported per batch unit.
• Fixed an issue introduced in QIAGEN CLC Main Workbench 7.8.1 where the Download Sequences from NCBI tool would continue to indicate it was searching when in fact the search had finished and no items were found.

Bug fixes

• Fixed an issue where the Search for Sequences at NCBI tool did not display the first and last search result in each page of results returned.

BLAST

The list of BLAST databases for use with the BLAST at NCBI tool has been updated:

• Added “RefSeq representative genomes” database.
• Removed “New or revised GenBank sequences (month)”. This is no longer supported by the NCBI.
• Changed “References mRNA sequences”name to “References RNA sequences”. The database that is searched remains the same as before.
• Changed “16S ribosomal RNA sequences” database to now search the  “rRNA_typestrains/prokaryotic_16S_ribosomal_RNA” database, as listed on the NCBI website. It previously queried “TL/16S_ribosomal_RNA_Bacteria_and_Archaea”.
• Fixed “Human genomic plus transcripts” and “Mouse genomic plus transcripts” databases configuration to reflect their new location. Searching these previously returned an error.

Metadata

• Usability aspects of data association using the Import Metadata tool have been improved, including adding a preview of data items to be associated with particular metadata rows.
• The speed of searches for data elements with associations to specified metadata, from within a Metadata Table, has been greatly improved. To enable metadata related searches to work after upgrading to the QIAGEN CLC Main Workbench 7.8, indices for the locations containing the relevant data will need to be rebuilt.
• A preview of data items that will be associated with particular metadata rows has been added to the Import Metadata tool.
• Various small usability improvements have been made to the Import Metadata tool.

New features and improvements

• Tutorial windows are no longer blocked when a wizard is open.
• An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
• When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms. This improvement affects the tools Hypergeometric Tests on Annotations and Gene Set Enrichment Analysis (GSEA).
• It is now possible to right-click on a table cell and filter table rows based on the value of that cell by choosing options under the new context menu section called  “Table filters”. This change applies to all tables where advanced filtering is available.
• Support has been added for ‘negative lookahead’ when using Java regular expressions when using the Motif Search Tool.
• In cases where tools within a workflow have been renamed, it is now possible to filter for original tool names within the workflow configuration view of the workflow editing tool.
• Various minor improvements

Bug fixes

• Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
• Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
• Fixed an issue with the Annotation Table view of a sequence where it was possible to change the types of annotations displayed at the same time as an annotation was being edited, which could lead to an error being thrown or the wrong annotation being changed.
• Fixed an issue with Primer Tables where an error resulted if either the option “Save Primer(s) Fwd, Rev” or “Save Fragment” was chosen and then the save operation was stopped by clicking on the Cancel button.
• Fixed an issue where in some cases filtering tables for empty values would not produce any results.
• Fixed an issue where advanced filtering did not work when looking for rows with cells containing multiple values using the filtering term “=” (equals).
• A sporadic java issue that led to errors including the text “java.lang.ClassCastException: sun.awt.image.BufImgSurfaceData cannot be cast to sun.java2d.xr.XRSurfaceData”, has been addressed through an upgrade to java. This issue was primarily seen when using the Workbench remotely on Linux systems.
• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST installed.
• Various minor bugfixes.

Retirement

• The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.

Other notifications

• An option to opt out of providing anonymous usage information to QIAGEN has been added to the Workbench Preferences. We are not yet collecting any usage information so opting in or out does not have any effect at this time.

Bug fixes

• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected Workbenches with the CLC MLST Module installed.

Improvements

• Updated the restriction enzyme list from REBASE.

Bug fixes

• Fixed an issue with running BLAST on macOS Sierra.
• Updated PFAM links reported by the Pfam Domain Search tool.
• Fixed an issue introduced in QIAGEN CLC Main Workbench 7.7.2 where enzymes listed alphabetically after RdeGBI were missing methylation information.
• Fixed a problem where launching a tool from the Quick Launch window after sorting led to the wrong tool being started.
• Various minor bugfixes.

Advanced Notice

Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed.

• Windows: Windows Vista and Windows Server 2008
• Mac: Mac OS X 10.7 and 10.8
• Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21

Workflows

• Workflow outputs can now be configured so that subfolders to contain the outputs are created.
• New placeholders are available when defining the names of workflow outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour}, {minute}, {second}.
• Placeholders within workflow output names that were previously available only as digits can now be specified using written names: {name} is a synonym for {1} and {input} is a synonyms for {2}.

• When using the {2} placeholder for custom naming in workflow output elements, only unlocked inputs will be included in the generated name.

• In the generated pdf showing all the configured parameters of a workflow, entries for parameters connected to a tool or an input element now list the names of the defining elements. Previously the parameter listings for such elements were left blank.

• Where a tool name has been altered in a workflow, the original name is now included alongside the changed name when exporting workflow parameters.

• The History view of data elements created using a workflow now includes information about the workflow that created them.

• The order of the tools in the workflow “Add Element” menu now matches the order in the Workbench Toolbox menu.
• Improved workflow validation to aid the user in identifying inputs that will be ignored due to the configuration of the workflow elements.

Launch

• The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.
• Analyses can now be launched on data elements listed in the results table of a Local Search by selecting the elements of interest, right clicking with the mouse and navigating through the context menu that appears.

Metadata

•  A “Remove Association(s)” option for removing metadata associations from selected data elements has been added sin the Metadata Elements view in a right click context menu.
• In the Metadata Find Associated Data view it is now also possible to use Find in Navigation Area when multiple rows are selected.
• When importing metadata from a spreadsheet with formulas in it, the result of the evaluation of the formula (as displayed in Excel) is now imported rather than the formula itself.

General

• All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
• The list of enzymes pre-installed in the workbench has been updated from REBASE.
• The option “is not in list” has been introduced as a new table filtering option.
• Read group details are now shown on the Element Info view of sequence lists.
• GenBank import now also allows for file names with ‘GBFF’ extension.
• The “Sort folder” tool now uses numerical sorting for filenames prefixed with a number.
• New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
• Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.

Bug fixes

• Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
• Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
• The Create New Sequence List button in a broken pair table now works when multiple read groups are involved.
• Fixed a bug that made graphics export of some plots from reports fail.
• The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
• Tables with more than 126 million entries now show a warning that they contain too much data to display instead of leaving the table empty.
• Fixed an issue where sequences of length zero would cause the Create BLAST Database tool to throw an error. Such sequences are now skipped and will not included in the final database.
• Fixed an issue in the wizard for the tool Create Entry Clone where a previously used data located on an unmounted location would result in an error message being shown.
• Fixed a rare issue where some annotations could, but did not necessarily, go missing on  sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option “Delete selection” was used.
• Fixed a bug in the “Manage Enzymes” wizard that prevented a user from cancelling the action if “Save as new enzyme list” was enabled.
• Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
• Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted.
• Fixed an issue where right-clicking on a graph in a report and choosing to show “Report”, “History” or “Element Info” triggered an error.
• Fixed an issue with links in tables to the PDB and dbEST databases.
• Fixed an issue where the save wizard dialog did not pre-select “Save in input folder” when that option was the most recently used one.
• Fixed an issue where the save wizard dialog did not pre-select “Save in input folder” when that option was the most recently used one.
• Fixed an issue where, when the Processes tab was hidden and then shown again, any processes listed before the tab was hidden were no longer shown.
• Fixed an issue that made “Download and save” fail when invoked on a Blast editor.
• Updated the URL to use for links to UniProt databases.
• Various minor bugfixes.

Bug fixes

• Fixed an issue that arose when executing workflows with multiple inputs in batch, where changes to pre-defined, fixed inputs specified during the launch process were not applied.
• Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
• Fixed an issue where sorting a folder while saving into it could trigger an error.
• Fixed a bug in the batch mode dialog that would lead to an error when problems related to the underlying file or data location were encountered.

Advanced notice

From the autumn 2016 release, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.

New tools

Import Metadata – basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.

Improvements

Metadata

• The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.
• It is now possible to change the type of a metadata column, even if it already contains values. Conversion is only possible when all existing values in the given column can be converted to the new data type.
• Usability enhancements in the Metadata Table Editor.

Workflow

• Workflow inputs  can now be ordered via the Workflow Editor, affecting the order that input information is requested when setting up a Workflow run.
  • Workflows with multiple input elements, where all input elements will be changed per batch, can now launched in batch by right-clicking on the installed workflow name and choosing the option “Run in Batch Mode…”.
• Tools in a Worfklow that have been renamed will have both the new tool name and the original tool name displayed in the Workflow Configuration Editor.

General

• Performance optimization for sizing phylogenetic trees by metadata
• The Download Pfam Database tool has been updated to download version 29.
• Improvements to the way Ensembl IDs are parsed to links in tables: stable Ensembl IDs are now correctly parsed to links for all Ensembl-supported organisms (Ensembl release 83).
• The options for saving the output from “batch jobs” have been improved. Outputs can now be saved into a specified single folder in addition to the other established save options.
• All Excel sheets in a document are now imported and each sheet has a table created for its contents.
• The CSV, HTML and Excel table/tabular exporter now use “Inf” and “NaN” values to replace the ambiguous “?”.
• In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
• An option has been added to allow the same print settings to be applied to all reports being exported to pdf format in a given export run.
• The “Manage Resources” tab has been removed from the the Plugin Manager.

Changes

Workflow

• The Create Scatter Plot tool is now Workflow enabled.
• The Create MA Plot tool is now Workflow enabled.

General

• Versions of individual tools are now reported in the history of output objects.
• Export to clc format now truncates very long filenames.
• Plots without any data points will now be skipped when rendering reports.
• RPM package installers for Linux are no longer available.
• Associate Data Automatically accepts data elements (not folders) as input.
• The ‘Database Fields’ label shown in the ‘Show Element Info‘ view has been renamed to ‘ Local Attribute Fields’.
• The “Metadata Role Override” parameter that was visible when creating Workflows has been removed.
• The user can no longer uncheck “export all columns” for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.

Bug fixes

• Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• In heat maps it is now possible again to show colors legend to the left and right of the heat map.
• Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
• Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
• Fixed an issue where an error was reported if the local realignment tool detected an insertion followed by a deletion in the original mapping. Such positions are now ignored.
• Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
• Fixed an issue where the “Show results”option in the Processes tab would lead to an error if the results dataset was very large.
• Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
• Fixed an issue where an error arose when renewing a borrowed network license.
• Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
• Fixed a bug that  led to the inclusion of the number of excluded batch units in the count of the total number of batch units to be processed.
• Added missing percentage signs for identities and gaps in Blast text exports.
• A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
• Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
• An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
• Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
• Fixed an issue with Open Copy of Workflow so it now works on all workspaces rather than just the first workspace.
• Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
• Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
• Fixed a bug that was causing missing report text lines.
• Fixed an issue where, when the option to “Skip these updates” was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
• Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
• Fixed an issue where sub-jobs were not resumed after pausing and resuming a batch process.
• Fixed an issue where the workflow installer creation keyboard shortcut could be used when it should have been disabled.
• Fixed a rare issue that could be triggered by switching editor view with a double click.
• Fixed an issue that caused the ‘Use random codon’ parameter in the tool “Reverse Translate” to report a null-error.

Plugin updates and fixes

All plugins need to be installed in the new Workbench for compatibility reasons.

Changes to freely available plugins

• Annotate with GFF: Now supports spaces in annotation names.
• Batch rename: Fixed an issue where a warning was displayed for entries not modified.

All changes in this release have also been fixed on the QIAGEN CLC Main Workbench 7.8.x and 7.7.x lines at time of writing, with the exception of the one release note marked with an asterisk. That issue was fixed for QIAGEN CLC Main Workbench 7.8.0 and will be fixed in future in the QIAGEN CLC Main Workbench 7.7.x line.

Improvements

• All NCBI server communication is now encrypted (uses HTTPS).
• Updated the URL to use for links to UniProt databases.
• Updated BLAST executables to be compatible with macOS Sierra. This change only affects Mac users.

Bug fixes

• Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option “Delete selection” was used.
• Fixed a bug in the Manage Enzymes wizard that prevented a user from cancelling the action if “Save as new enzyme list” was enabled.
• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST Module installed.*

Bug fixes

• Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
• Fixed a bug that made the help for tree side panel settings inaccessible when the workbench was run in limited (evaluation) mode.

Advanced notice

From the autumn 2016 release, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.

Improvement

• Performance optimization for sizing phylogenetic trees by metadata.

Bug fixes

• Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
• Bug fixed causing missing report text lines.
• The Download Pfam Database tool has been updated to download version 29.
• Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
• The “Metadata Role Override” parameter that was visible when creating Workflows has been removed.
• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• Fixed an issue that caused the ‘Use random codon’ parameter in the Reverse Translate tool to report a null-error.
• Fixed bug when download buttons on BLAST result table view failed for nucleotide sequences.
• Fixed an issue with renewing a borrowed license.

Bug fixes

• Fixed a bug when the “Search for sequences at NCBI” tool would fail to download nucleotide sequences with the error message “The following sequences were not downloaded correctly: …”.
• Fixed a problem with the BLAST at NCBI step of the Create Protein Report tool.
• Fixed an issue leading to an error during VCF export where the data involved had originally been imported from VCF files and the values in the QUAL field were integers.
• Export of floating-point (decimal) numbers to VCF format were previously dependent on the specified locale. This has been fixed so that the decimal separator now always is a point.
• When doing automatic association of metadata, the log now shows which metadata rows were not associated with any data.
• Fixed a bug that prevented metadata manual information to be accessed from within the Workbench.
• Fixed a bug where doing automatic association using a metadata table stored on a CLC Server would fail.
• Automatic association of metadata now handles association based on the a prefix of data names rather and exact matching to the whole data name.
• A metadata table no longer needs a key column for its rows to be manually associated with data elements.
• An option to override metadata roles previously visible in the configuration of Workflow outputs was removed.
• Fixed issue that caused locked parameters to be overwritten by a previously entered value, during workflow execution.
• Fixed an error happening when a Workbench Data Location was pointing at a file on the system instead of a folder. It will now appear as unavailable in the Workbench Navigation area.
• Enabled tooltips for all parameters when configuring and executing workflows.
• The login process from a Workbench to a CLC Server must now complete before opening a clc url will begin.
• Fix a problem on Macs where the Workbench was not recognized as a custom protocol handler for clc:// urls.
• Resolved a rare occurring exception that could be triggered by switching editor view with a double click.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).

New features and improvements

• Batching on selected elements is now possible: it used to be restricted to selected folders.
• One can now select “EST” as database when using the Search for Sequences at NCBI tool.
• The Hierarchical Clustering of Samples tool can now be executed as part of workflows and on the server.
• Improved memory management when handling large report elements.
• Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
• Numbers are no longer appended to the names of Workflow elements when creating a copy of a Workflow using “Open Copy of Workflow”.
• Metadata Management. Keep track of input files and import meta information for your samples.

Bug fixes

• Fixed a rare occurring issue where the Workbench would display an error message when installing a 3rd party licensed plugin.
• Fixed an issue where selecting an entry in a Blast results table could highlight the wrong alignment in the Blast editor if the table had been filtered or sorted.
• Fixed an issue where clicking on an annotation in the Design Primers editor could give rise to an error message.
• Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
• Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
• Fixed exported reports having the wrong author in certain situations.
• Fixed an issue whereby Create Box Plot and Principal Component Analysis could sometimes be run with illegal arguments, leading to an error message.
• The output of the Reverse Complement Sequence tool now gets the suffix -RC attached to the name of the input instead of -1 before.
• Fixed a bug in the Predict Secondary Structure tool when the option to calculate the partition function was selected  for long molecules (>1000 nucleotides).
• Fixed an issue where one could not zoom in after zooming out fully on very large workflows.
• Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
• Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

Bug fixes

• Added a work around to a java issue that occasionally resulted in the Workbench displaying an uninformative error and requiring a restart to continue working.
• Fixed an issue with running BLAST at NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of “no hits” was being reported instead.
• A fix was applied to avoid an exception in circumstances when the cleanup of downloaded files from BLAST failed.
• The Reverse Translate tool ignored any genetic code specified in the codon frequency tables. All reverse translation would thus default to the standard genetic code.
• When installing a workflow with bundled data, it is no longer possible to select a read-only folder for storing the data.
• Fixed wrong display of “Supported format” when exporting elements from either the Folder Editor or the Local Search Editor.
• Fix of potential wrong file being saved when editing a file found via the Local Search Editor.
• Plots inside reports are now shown with their saved side panel settings.
• Fixed saving different line colors in plots through the side panel.
• Side panel option to show legends for a plot with more than 10 samples is now enabled.
• Fixed an issue that led to an error when rendering plots for empty data sets.
• Fixed an issue where the “Empty Recycle Bin” option was sometimes incorrectly unavailable.

New features and improvements

• BLAST has been upgraded to BLAST+ 2.2.30 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.30 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777
• The GTF exporter is now available for the Main Workbench.
• Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
• Improved Excel, HTML and tab delimited export of variants (choose only the annotations/columns you need).
• The results of BLAST searches now include a new view, the Blast Hit Table.

Bug fixes

• Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of “no hits” was being reported instead.
• Fixed an error affecting the “Cut Sequence Before/After Selection” tool in the Cloning editor.
• Fixed bug where a left-click quickly followed by right-click was interpreted as double-click on OS X (in the persistence search result list, in the toolbox tree, and in the workflow editor).

New features and improvements

• Tracks:
  • Consistent output when enriching variant tracks and annotation tracks with extra table columns. Output tracks from these tools now have the same number of added table columns and the columns will always be in the same order. Previously, if an added column had empty values for all variant rows, it would have been removed from the final table, resulting in varying number and relative order of additional columns when multiple samples were processed with the same tools/workflows. All columns are retained now, facilitating downstream processing of exported tables, and providing immediate visual reference as to which enrichment/annotation tools have been applied, even if they did not produce any results for a particular sample.
  • Tables for variant tracks and annotation tracks can now sort and filter columns with cells containing multiple numbers.
  • Improved the track viewer for variant tracks to show the sequence alteration on the rendered variant.
  • Graph tracks now show negative values filled upwards to y=0 (as expected).
  • Increased decimals for numbers when exporting table to CSV, tab delimited text, and Excel.
  • Improved reporting of errors related to low disk space.
• Workflows:
  • When installing a workflow in the workflow manager, the newly installed workflow is automatically selected.
  • The “Run” button in the workflow editor does not require a saved workflow anymore to be enabled.
  • In the execution wizard of a workflow the “Reset to default” button is now active.
  • All icons in the workflow editor are now on the left side.
  • Introduction of snippets: Parts of workflows can now be saved as a snippet and reused in other workflows.
  • Installed workflows: It is now possible to create a copy of an installed workflow and open the copy in the view area by clicking once and then right-clicking on the installed workflow in the toolbox. This brings up the option “Open Copy of Workflow”.
• New features for the 3D molecule viewer:
  • Align to Existing Sequence makes it possible to connect a 3D protein chain to a sequence, sequence list, or an existing alignment.
  • Transfer Annotations makes it possible to create atom groups from sequence annotations (and vice versa) for connected sequences.
  • Improved layout of the property viewer.
  • Improved PDB import of water molecules, DNA/RNA, and saccharides.
  • When importing PDB files, the resulting Molecule Project now contains citation information (PDB ID and primary reference), which can be found in the ‘Show History’ view.
• MA plots, scatter plots and histograms can now accept expression tracks as input.
• Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.
• The External Application Client Plugin is now available directly from the Workbench Plugin Manager.

Bug fixes

• Fixed display problem in read mappings showing too many hidden insertions (as vertical black lines) in certain overlapping paired reads.
• Fixed problem with links and text in tables that were being cut off when succeeding a link.
• Restriction site analysis: The values “Cut position(s)” column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
• Workflows:
  • In the workflow editor the “Reset to default” now always reverts to the right names.
  • In the workflow editor the validation is now correctly triggered when changing the configuration of an input element.
  • The workflow editor can now open workflows in which the graphical view of the workflow is corrupt.
  • Fixed an exception which could occur during workflow migration.
  • Data with the same name can now be bundled multiple times in a workflow installer.
  • Previously when a plugin contained custom actions and a workflow, the workflow could not be installed. This has been fixed.
  • Fixed problem with unlocked output names that previously could not be configured during execution of a workflow.
  • A workflow with configured data from a server is now automatically validated when connected to the server (when opened in the editor). Previously the workflow had to be closed and reopened first.
  • The original workflow file included in a workflow installer can now be exported directly without having to restart the workbench in advance.”

• A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.

•  Fixed an error that could cause batch processing to open all results rather than saving them.

• Fixed problem going back in the wizard for the “Find Binding Site and Create Fragments” tool.
• Fixed error occurring when removing an unsaved reads track from a track list.
• Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
• Fixed error when showing protein translations of annotations shorter than 3 bases.
• Search for PDB Structures at NCBI has been fixed to correctly show PDB deposit date and organism type.
•  Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool.
• Hypergeometric test on annotations: Fixed a rare error that occurred for some datasets containing annotations of the form: ‘1234 // abc’.
• The alignment editor view and alignment primer design view now have independent settings.

Plugin updates and bug fixes

• TRANSFAC Plugin updated and now has two modes of operation: “Classic” and “Genomic”. Classic mode is the legacy mode taking sequences as input and annotating these sequences. The new Genomic mode takes regions on a genome (an annotations track) as input. In addition, in both modes it is now possible to specify global thresholds of similarity score which can be used to filter the annotations included in the output.
• A bug has been fixed with import of metadata containing column names with colons in the Metadata Import plugin.

Bug fixes

• Fixed an issue that caused the Reverse Translate tool to ignore the genetic code specified in the codon frequency tables such that the reverse translation used the standard genetic code.
• Fixed saving different line colors in plots through the side panel.
• Plots inside reports are now shown with their saved side panel settings.
• Side panel option to show legends for a plot with more than 10 samples is now enabled.
• Fixed an error that occurred when hovering the mouse cursor over the edge of a read mapping.
• Read-only folders are no longer offered as potential locations to save data bundled with a Workflow.

Bug fixes

• Fixed an error affecting the “Cut Sequence Before/After Selection” tool in the Cloning editor.
• Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of “no hits” was being reported instead.

New features and improvements

• It is now possible to run a workflow without an optional input.

Bug fixes

• The AAC tool did not annotate variants in 3′ UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation.
• Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data.
• Fixed a bug in the ‘Maximum Likelihood Phylogeny’ tool that failed when generating bootstrap values for certain input alignments.
• Fixed problem with scrolling to the relevant files when selecting objects as parameters in tool wizards.
• The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
• Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
• It is now possible to run a workflow without an optional input.

New features and improvements

• Workflows:
  • The input information is now shown in the preview dialog and also exported to all formats.
  • It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
  • Workflows as such can have multiple inputs (though this will disable the batch functionality).
  • Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
  • A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
  • A text field has been added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
  • A new editor was added to the workflow to make it easier to check the configuration. The new editor can be accessed from the lower left corner of the View Area and lists all configuration parameters.
  • Workflows can be packaged with a plugin and will get installed with the plugin simultaneously.
  • Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable from workflows installed in the workbench.
  • The execution of a workflow in the workbench and on the server have been unified to have the same behavior regarding logs, intermediate results and output naming.
  • Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, all parameters are displayed.
• Protein Analysis, Pfam domain search:
  • Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool “Download Pfam Database”.
  • Searching multiple sequences is significantly faster.
  • New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.
• 3D Molecule Viewer:
  • Protein Structure Alignment – high quality structural alignment of whole protein chains or selected regions of a protein, available from the Side Panel of Molecule Projects.
  • Project Tree improvements – new ways of selecting nearby atoms. Improved visualization of intermolecular bonds. Atom groups are now stored on the Molecule Project and can be renamed. Labels on custom atom groups now show residue names if applicable.
  • New molecule color scheme where only the carbon atom color is varied.
  • 3D view state – all 3D visualization settings (including custom atom groups) can now be stored on a molecule project and shared with others.
  • Molecule Preparation. Many improvements, including better handling of partial charges and more recognized chemical groups.

• Local Search enabled from the menu bar now includes filtering on “Path”.
• Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
• Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
• The tracks info panel, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
• Saving/applying side-panel settings for tables now works for different tables that share some columns.
• Copy operations can now be stopped.
• Output from “Reverse Translate” can now be a Sequence List.
• Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
• CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
• Improved error message in the Empirical Analysis of DGE tool in case of invalid expression values in experiments (occurs rarely).
• More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
• Genetic codes: The list of NCBI translation tables has been expanded to include  translation table 25 “Candidate Division SR1 and Gracilibacteria” (See: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c).
• Improved error messages due to low disk space.

Bug fixes

• Translation of CDS annotations to protein sequences was wrong in cases where the reading frame was not +1 or -1 in CDS annotations imported from ENSEMBL. This error affected the Translate to Protein tool, translation functionality in sequence viewers and their context menus, as well as the Amino Acid Consequences (AAC) variant annotation tool. We highly recommend redoing the AAC analysis for correct variant annotation, as CDS tracks typically are created from ENSEMBL data.
• The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
• Icons in the workflow editor are now scaled consistently when zooming in or out.
• Several issues with the validation display in the workflow editor have been fixed.
• A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
• Fixed problem where the “space” key did not trigger “Find Conflict” in the stand-alone read mapping editor.
• Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
• ‘Replace input sequences with result’ in Cloning Editor no longer fails.
• Multi-sequence BLAST search results (BLAST tables) are now exportable as plain text.

Changes

• Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

Bug fixes

• Fixed error that caused selections in views not to be centered in the middle of the view.
• Fixed bug that caused a crash in the Reassemble Contigs tool
• Fixed bug that made the Workbench crash when viewing tables under certain circumstances
• Fixed problem with “Find” on stand-alone read mappings with a circular reference and sequence lists containing circular sequences.
• Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow.

Bug fixes

• Fixed problems causing an error when trying to uninstall plugins.
• Fixed issue with pausing and resuming running processes

Improvements

• Fasta export:
  • Fasta export with trimming is now much faster and consumes less memory
  • Fasta export now reports progress while executing
  • When the “Remove trimmed regions” option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
• Translate to Protein (Batch Process):
  • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
  • The log has been made more detailed and informative
  • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
  • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
• The PDB importer has improved support for custom residues

Bug fixes

• Fixed missing icon for “Metadata Import” in the phylogenetic tree table
• Multi BLAST results table: the missing “Description (E-value)” field is displayed again in the table output
• Fixed a bug that made PDB import fail on workstations with Turkish Locale settings
• The tool “Restriction Site Analysis” ignored the selected number of cut sites in GWB 7.0. This has been fixed

New features and improvements

• New functionality for phylogenetic trees (was previously part of a beta plugin)
  • Greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of the trees.
  • Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees.
  • Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.
  • Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
  • Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.
  • Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
  • Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
  • A user defined start tree can now be supplied to the ML inference tool.
• Complete redesign of the graphical user interface including:
  • New tool bar graphics
  • New product logos and colors, including splash screen
  • New background graphics on canvas and in dialogs
  • Tool bar has been re-organized
  • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
• New concept for Side Panels and Views:
  • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
  • Side Panels now consist of palettes that can be organized in group and the order can be customized
  • Palettes can be detached and placed anywhere on the screen
  • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
• Zoom tools redesign:
  • The zoom tools have been re-organized and placed closer to the data
  • A zoom slidershows the present zoom level and can be used to adjust zoom
    • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.
  • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.
  • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.
• Copying data in the Navigation Area runs much faster and uses less memory than before. This is a great improvement which also kicks in when moving data between a QIAGEN CLC Genomics Server and a Workbench.
• Workflows:
  • Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
  • Workflows can be added inside a workflow. The inner workflow is “unfolded” into the single elements.
  • Parameters can now be renamed in the editor by the creator during configuration of the elements.
  • Workflows with invalid/unknown elements are laid out nicer and more consistent.
  • The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
  • Fit Width now fits the entire workflow in the editor by zooming out.
  • The sidepanel has a new section “Minimap” which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
  • One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
  • Better validation when configuring parameters in workflows
  • If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
  • The name of an output in the workflow can be set by configuring the output element
  • Parameters of a workflow run can now be exported to various formats via the wizard
  • It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
  • In the workbench the installed workflows are now sorted alphabetically.
  • The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
  • A cpw file can now be dragged into the workflow manager and will be installed.
  • Further speed improvements on working with larger workflows in the editor
  • New tools that are now workflow-enabled:
    • All tools in Statistical Tests
• 3D structure viewer:
  • Property viewer – a new tab in the Side Panel. Shows detailed information about the atom under the mouse pointer. If multiple atoms are selected (Ctrl-click), the distance (two atoms selected), angle (three atoms selected), dihedral angle (four atoms selected) formed by the selected atoms, is shown in the Property viewer. If a molecule is selected in the Project Tree, meta-data relating to the molecule is shown in the Property viewer.
  • Issues List. Issues related to the molecule structures and their chemistry representation is listed in the Issues List view on Molecule Projects. If seen in split-view with the 3D viewer, a selected issue will zoom to the atoms involved in the issue and select them in the 3D view.
  • General improvements to the PDB importer
  • Double-clicking an entry in the Project Tree will zoom-to-fit on the molecule or atom group.
  • When selecting atoms (by mouse clicking or from sequence), the atom context (whole residue or molecule) will also be shown in the 3D view. From context menu on ‘Current’ selection, an atom group can be generated either from the exact selection or from the selection plus the context (whole residues or molecules).
• Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
• When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
• Trim annotations can be used to trim off sequences when exporting to fasta.
• Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak’s fraction of the maximum peak height.
• Advanced table filter now includes an option to search for “starts with” in addition to just “contains”
• Limitations on export of Excel 2010 files (xlsx) are removed:
  • Multiple tables can be exported to one xlsx file
  • Reports can be exported to xlsx
  • Hyperlinks are preserved in xlsx files
• SignalP prediction has been updated to be server-, batch- and workflow enabled.
• Folder contents view: subfolders will display how many items they have
• Assemble Sequences tools now accept sequence lists as input.
• REBASE restriction enzyme list updated to version 310.

Bug fixes

• Workflow:
  • In the editor the “Fit Width” zooming was active, but behaved as “100%” zooming. Therefore the “100%” zooming is now active instead of the “FitWidth”
  • Added or connected elements are now placed near where you connect or add them, even when zoomed near or far.
  • It was possible to Undo the action of adding a workflow output, but it was not possible to Redo afterwards.
  • The right-hand icons in an element now scale with zooming.
  • The log of a workflow run on the server contains now the same information as when run in the workbench.
  • When configuring elements in the editor, the “Reset to CLC Standards” button is now functional and will reset the parameters to their default values. When configuring during installation or execution the button is disabled.
  • The log of a server executed workflow now states when the workflow has been cancelled.
  • A workflow with elements which provide additional inputs could not be batched.
• Crash when adding data to experiments (e.g. by running any of the statistical analysis tools) has been fixed.
• Various bugs in the extract consensus sequence tool have been fixed.
• When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
• A problem with filtering and sorting the BLAST output table has been solved. Some of the columns were treated as text instead of numeric.
• Restriction maps, histogram data, and primer tables could not be exported to csv or similar. This has been fixed.
• When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.
• Fixed problems with Excel export that failed when special characters were used in the name.

Changes

• The two tools in the “Multiplexing” folder in the toolbox category have been changed:
  • “Process Tagged Sequences” has been removed..
  • “Sort Sequences by Name” has been moved directly into the Sequencing Data Analysis folder.
• Motif search: annotations created by the motif search are of type “Motif” instead of “Region”

New features

• Heat maps: It is now possible to show a legend on a heat map.

Changes

• When importing Genbank nucleotide sequences, the Workbench will determine whether it is DNA or RNA based on the sequence rather than the description in the file.

Bug fixes

• Fixed: Trimming sequencing data for vector contamination from UniVec failed
• Fixed: GFF export failed.
• Fixed: Copying information from the Folder Contents view did not work.
• Fixed: out of memory error when performing bootstrapping with ML tree construction methods.

Bug fixes

• Fixed problem in workflows: it was not possible to configure all elements when running a workflow that branched after the input element.

Bug fixes

• Description text in progress area is now making full use of available width of the progress area
• Handling of line breaks in annotation notes improved
• On Linux: User interface text has been changed to not use bold font to make a better visual appearance
• Annotation tracks and variant tracks created in QIAGEN CLC Genomics Workbench can be displayed in a table

Improvements

• Fragments generated from restriction site analysis can now be opened in batch. When multiple rows in the fragment table are selected, the right-click menu option will now create a sequence list with all the selected fragments.
• For alignments, mappings, BLAST results and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.

Bug fixed

• Several errors related to workflow configuration and execution have been fixed.
• Errors related to managing Workspaces have been fixed.
• Annotations were added by the Find Open Reading Frames tool, even though the option to add annotations was not selected. This is now fixed.
• Fixed an out-of-memory problem in the Create Alignment tool.

Improvements

• Added Legal and Tabloid formats for printing

Bug fixes

• Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
• Various minor bug-fixes

New features

• Workflow: there are several important new features for workflows
  • It is possible to control which parameters should be locked or unlocked. This means that the creator of the workflow can decide which parameters should be left open for adjustment when the workflow is executed.
  • Usability of workflow editor greatly improved
    • There is a grid for helping layout
    • Visual indication of the number of possible connections as input to a workflow element
    • Visual indication to show if parameters have been changed
    • Handles for dragging and connecting elements have been made more clear
    • Side Panel for controlling grid layout and switching on compact visualization of workflow elements
    • You can high-light selected paths in a workflow
  • It is now an option to attach the workflow design file with the installer to allow users edit the workflow
  • There is a special icon for workflows in the Toolbar to make the creation and installation of workflows more visible
  • Several tools are now workflow-enabled:
    • Find Open Reading Frames
    • Translate to Protein
    • Convert to RNA
    • Convert to DNA
• Toolbox improvements:
  • New Favorite Toolbox: A new tab next to the Toolbox holds
    • Frequently used tools. This is automatically updated based on which tools are used most frequently.
    • Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
  • Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
• Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
• Performance when sorting of large tables has been improved
• Rename can now be done through right-click menu in Navigation Area.
• Annotations on circular sequences:
  • When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
  • When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
• Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
• Find Open Reading Frames can be run in batch and workflows
• Translate to protein can be run in batch and workflows
• Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
• Alignments can be used as input for finding primer binding sites.
• Export now has progress and can be canceled.
• BLAST results and 3D structures can be exported as text.
• Batching: Previously, results where saved in the same folder as the input data. This can now be changed and a new save folder can be specified. Sub-folders will be created for each batch unit.
• The limit for the cloning editor has been increased to 6,000,000 bases (from 4,000,000 bases).
• Create Expression Clone (LR) from Gateway Cloning produces sequence object rather than a list
• Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
  

  Bug fixes

  • Fix to the proxy settings recognition meaning that Download of BLAST databases now work when there is a proxy setup.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Fixed a problem sorting sequence lists on modification date.
  • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
  • Various bug fixes.

Bug fixes

• Fix to the proxy settings recognition meaning that download of BLAST databases now works when there is a proxy setup.
• Fixed problem of not correctly formatting qualifiers in EMBL export.
• Fixed a problem sorting sequence lists on modification date.
• Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
• Various bug fixes.

Bug fixes

• Fixed: Workflows would fail when intermediate results were empty (e.g. if no variants were found and a variant track was used for subsequent analysis).
• Various bug fixes

New features

Workflow

• Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
• In the first release, the gateway cloning tools are the only tools that can be incorporated into workflows.
• Workflows can be distributed and installed either in the Workbench or in the QIAGEN CLC Genomics Server
• The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
• The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
• Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

Plugin updates

Grid integration plug-in is integrated into the general server plug-in. If a grid preset is present on the server, the Grid option becomes available in the Workbench dialog.

Improvements

• Support for Mac OS X 10.8, Mountain Lion

Bug fixes

• Fixed: Problem with online BLAST at NCBI

Improvements

• Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.
• The license order ID is visible in the License Manager, both for static and network licenses. For security reasons, the last 10 characters of the ID are masked. This will prevent unauthorized persons from copying the license order ID to another computer, but will allow the CLC staff to identify the license used.

Bug fixes

• Fixed: Cloning bug: when performing restriction cloning in regions with single-stranded DNA, you would get an error.

New features

Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins It is now possible to specify the number formatting in tables in the View Preferences.

New features

• Printing and pdf export of assemblies: the assemblies are now wrapped to make better use of the paper.
• Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
• “Show” submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
• The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
• The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.
• VectorNTI import is no longer in a separate plug-in but part of the Workbench. The functionality remains unchanged.

New plug-ins and plug-in updates

• Additional Alignments Plug-in updated
  • The algorithms have been updated to the most recent versions
  • The list of algorithms has been reduced to two for compatibility reasons

New plug-ins and plug-in updates

• MLST module updated
  • Possible to download MLST schemes from any web site compatible with mlstDBnet
  • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than “New allele”

See a list of all plug-ins here.

New and improved features

• Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning
• Process tagged sequences
  • A summary report is now available with an overview of the number of reads per bar code
  • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol
• Find Binding Sites and Create Fragments improved:
  • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G)
  • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table)
• Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read

Bug fixes

• Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line
• Fixed: Set-up experiment would crash when using many samples
• Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis
• Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed
• Fixed: Motif search did not exclude regions with Ns when the option “Exclude matches in N-regions for simple motifs” was selected

New and improved features

• You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad
• Translation in the Side Panel of nucleotide sequences now includes options to translate “All forward” or “All reverse” reading frames
• Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position
• Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment
• Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list
• Restriction enzymes updated with latest REBASE version
• Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu

Bug fixes

• Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules
• Fixed: Experiments tables can now be exported in Excel and csv formats
• Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of QIAGEN CLC Main Workbench 6.0
• Fixed: Pattern discovery wizard failed when the tool is run for the second time
• Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format

Bug fixes

• Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
• Fixed: The UniProt search has been updated to reflect URL-changes at uniprot.org
• Fixed: A problem with microarray experiments where large experiments could not be analyzed

New and improved features

• All history entries will from now on include the version number of the software
• Performance of Excel 2010 exporter improved in terms of speed and memory requirements
• When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server
• BLAST
  • BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
  • The “Mask lower case” option has been removed
  • Tool to download BLAST databases from NCBI within the Workbench

Bug fixes

• Fixed: Alignment-based primer design failed for columns with many gaps
• Fixed: “Find Binding Sites and Create Fragments” did not find binding sites where the primer extended the 5′ end of the template sequence
• Fixed: Import of certain special Genbank files failed
• Various minor bug fixes

New and improved features

• Local BLAST is faster when blasting against small databases

Bug fixes

• Fixed: Local BLAST did not work on Mac OS 10.5
• Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor
• Fixed: Import of GO annotation files did not work
• Various minor bug fixes

Bug fixes

• Fixed issue with synonymous overhang characters in cloning editor
• Graphics export now works with restriction sites shown
• Gene Ontology Annotations can now be imported
• Improved support for Mac OS X systems with japanese language
• Improved support for systems with 512 MB of memory or less
• Blast: Fixed issue with BLAST database creation taking too long under certain circumstances
• Blast: Fixed issue concerning errors when input sequence names contained illegal characters
• Blast: Fixed issue with Extract And Open option being erroneously disabled
• Blast: Option to enter custom Entrez Query limits in Blast at NCBI re-introduced
• Blast: Improved speed when using Blast results as input to wizards

Improvements

• Cloning tool re-designed to make it easier and faster to perform restriction cloning
  • Restriction sites used to select target vector and fragment
  • Sequences can now be displayed in circular mode in the cloning editor
  • Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences)
  • Option to clone several fragments and adjust overhangs and orientation in one dialog
  • New cloning tutorial available for a quick introduction
• BLAST tools have been redesigned
  • New Blast Database manager for easy administration and management of local BLAST databases
  • More user-friendly way of creating and accessing local BLAST databases
  • Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets
  • The SNP Annotation using BLAST tool has been discontinued
  • See migration notes for using your old databases
• Improved layout of restriction site annotations
  • Linear view: There is a new option for displaying labels as “Stacked” which means that the labels of overlapping cut sites can be discriminated
  • Circular view: There is a “Radial” option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout
• Improved layout of general annotations
  • Linear view: There is an option to separate restriction sites and annotations in separate layers
  • Circular view: There is a “Radial” option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout
• Motif search available in Side Panel
  • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites)
  • Use motif lists to add your own motifs to the Side Panel
• Annotation table now available for sequence lists, contigs, BLAST results and alignments
• Batching functionality available for selected tools
• Multiplexing: Process tagged sequencing data
  • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples
  • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses
• Support for exporting tables as tab-delimited files
• Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog)
• The default database of restriction enzymes can be expanded (requires manual edit of database file)
• The default set of codon frequencies can be expanded (requires manual edit of table files)
• Improved option to export and import Side Panel settings
• Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB

Bug fixes

• The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules
• Various bug-fixes

Improvements

• Improved performance of table filtering. Removed limit on the number of rows that can be filtered.
• Option to search for read names in contigs (and also sequence lists and BLAST results).
• Improved performance of conflict table view of contigs.
• Better layout of graphics export and printing of contigs results: reference and consensus sequence repeated to provide an orientation context on all pages.

Bug-fixes

• Fixed error when opening tables generated by the Transfac plug-in and the primer search tool
• Fixed problem updating preview in Gateway cloning dialog
• Genbank export of annotations on the negative strand were not in the right order
• Fixed problems regarding editing and viewing of contigs and alignments
• Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
• Various minor bug fixes

New features

• Improved memory management in general: lower memory footprint and shorter management overhead pauses.
• Improved memory handling of large tabular data sets.
• Improved consistency of data handling including faster listing of folder contents
• Performance when saving small files significantly improved
• Performance of ACE export improved, especially for long reference sequences or read mapping tables.
• Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
• Improved performance of reading data files from shared drives.
• REBASE collection of enzymes updated to latest version
• BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
• Process tagged sequences: it is now possible to input barcodes on a comma-separated list. Read more
• Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
• Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1’000’000 or 1 000 000). Read more
• Normalization of expression data: it is now possible to do “Reads per 1,000,000″-style normalization of count-based data. Read more
• New preference group called “Data” to hold information about adapter sequences and Gateway cloning primer additions. Read more

Bug-fixes

• Print of folder content now takes settings in the Side Panel into account
• Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
• Better memory handling in conflict table
• Find in Side Panel: space are now allowed
• Genbank import: sequence name (LOCUS) was truncated to 18 characters

Bug fixes

• Fixed error concerning naming of dots in PCA plot
• Error in folder editor that prevented all elements to be shown is fixed.
• Documentation on trim using quality scores has been updated
• Fixed error preventing manual editing of contigs under special circumstances
• Various bug fixes

New features

• Expression analysis:
  • Volcano plots: you can now choose the values to plot on the x-axis. Choose between “Difference” and “Fold change”. Read more…
  • Table view of bar plots shows the same intervals as are shown in the bar plot.
  • Generic importer for expression array data in tabular format. Read more…
  • Generic importer for expression experiment annotation data in tabular format. Read more…
  • Gene Ontology (GO) files can now be used to annotate an expression experiment. Read more…
  • Tag profiling: You are no longer allowed to annotate tag samples, only experiments
  • Side panel of experiment table has been re-organized to provide better overview. Read more…
• Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
• Deployment
  • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more…
  • Support for removing tools accessing the internet (NCBI BLAST, update notifications etc). Read more…
• General import and export
  • Support for import of complex regions from GFF files
  • Export tables and reports in Excel format.
  • Import section of user manual re-structured to provide better overview. Read more…. Expression data importers are now described in technical details in a separate section. Read more….
  • You can now export multiple sequence lists in fasta format
  • Forced import of zip files is now supported (it will force import the contents of the zip file)
  • The standard import now accepts gzip and tar files as well as zip
  • If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
  • Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
  • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
  • When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
  • GFF plug-in has been updated to accept complex annotations
• Miscellaneous
  • Advanced retyping of annotations using the annotation table. Read more…
  • Improved reporting of situations when a full disk prevents saving of data
  • Downloading sequences using drag and drop from the search table no longer creates a “Downloading…” node in the folder. The download process can be monitored in the Processes tab.
  • Primer design now supports PCR fragments longer than 5000 bp.
  • Extract Sequences moved from File manu to Toolbox-> General Sequence Analysis. Read more…
  • Better progress feedback on various dialogs

Bug-fixes

• Fixed problem displaying the “Copying…” label when copying data and then updating the folder
• Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).

New features

• Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
• Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
• In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu.
• Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments.

Bug fixes

• Various bug fixes

New features

• Create new contig from selection
• Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
• Advanced view of elements in a folder including batch editing.
• Heat maps and clustering improved:
  • You can now perform different clusterings on an experiment and save them all. In the Side Panel you can switch between the different clusterings to show the corresponding heat map.
  • Terminology change in the clustering dialogs: “similarity measure” and “cluster distance metric” are replaced by “distance measure” and “cluster linkage”, respectively.
• Annotating samples or experiments for expression analysis:
  • This is now possible even if the number of features doesn’t match the number of annotations
  • You can now decide which column in the annotation file to use for matching to the sample or experiment. Because of this extra option, you can no longer include an annotation file when setting up an experiment. You need to add the annotations afterwards
• Microarray import improved:Added support for import of more versions of native Illumina BeadChip and GEO expression files
• Extract sequences improvements
• You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
• “Find” in text view now accepts Enter as command to find the next hit
• Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
• Export of annotations in GFF format (note that annotations with joined regions are not supported)
• Export of sequence data in fastq format
• Now possible to perform detailed manual editing of contigs with up to 100,000 reads
• Improved performance when zooming large contigs displaying a coverage graph

Bug fixes

• Microarray import: Fixed a bug that prevented import of expression data with white spaces in column names.
• Problem when adding annotations to an Illumina array file
• Fixed problems importing expression annotation files
• Fixed tblastn numbering issue
• Fixed problem with graphics export of contigs
• Problem rendering scatter plots without lines
• DNA strider files could loose name upon import
• Rare misplacement of annotations when editing very large sequences
• Various bug-fixes

This update is recommended for all users.

Data formats

• Data generated with version 5.1 cannot be read in earlier versions

New features

• Implementations of statistical tests for comparing expression levels of count-based expression measures as may be produced in RNA-seq
  • Kal’s test for differences of proportions in single sample to single sample comparisons.
  • Baggerley’s test for differences of proportions in two groups with replicates comparisons.
• “Reverse Contig” has been renamed to “Reverse Complement Contig.” Functionality is un-changed.
• Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates
• Import of Illumina expression bead arrays and bead array annotation files
• Import of Affymetrix Chp files (CHP / PSI)
• Transformation of expression values now supports square root transformation.
• Better feedback on processes: there is a tool tip showing details and start time.
• Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
• Much improved memory performance and processing time of large data sets
• Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
• Output and error log files are now placed in the application data directory in the user home

Bug fixes

• Fixed error when parsing files from Clone Manager (cm5-files)
• UniProt search works again

Updates

• Corrections to the ACE export
• Better performance of files with many annotations
• Fixed an error in RNA Structure Evaluation
• Fixed error and improved performance of Join Sequences tool
• Fixed error in Find Binding Sites on Sequence: no longer distinguish between lower and upper case
• Various bug fixes

Updates

• Find in the Side Panel did not support spaces when searching for annotations
• In the cloning editor under special circumstances, an error occurred when replacing a selection with fragment
• Sequence statistics codon count were not correct when using sequences
• Fixed error when deleting a selected read in a contig
• Fixed error in experiment table under certain sorting and filtering combinations
• Fixed error when exporting alignments in aln format

New features

Expression analysis including digital gene expression

• Support for both microarray- and sequencing-based (RNA-Seq) expression data
• Visualization: Interactive heat map, table and scatter plot views
• Transformation and normalization tools
• Quality control tools including principal component analysis, MA- and boxplots
• Experimental design tools for two- or multiple group comparisons
• T-tests and ANOVA analysis with support for paired/repeated measures
• Multiple testing corrected p-values (Bonferroni and/or FDR)
• Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
• Ability to import NetAffx annotation arrays and adding annotation to experiments
• Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. ‘GO’stats or specific protein pathways).
• Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results

Assembly

• Right-clicking a graph (e.g. coverage) on a contig lets you export the data points to a csv file.
• Multiplexing – Process Tagged Sequences now has an option to filter away groups with few sequences. This is an advantage if you have very ambiguous barcode definitions where sequencing errors would lead to a lot of “false” groups. These groups can now be filtered because of their small size. (The option is called “Minimum number of sequences” and is found in the third step of the wizard.)
• Importing assemblies with more than one contig creates multi contig tables (ace and cas file import)

Improved user experience of processes

• Non-modal feedback from processes:
  • When there is a message (e.g. from a BLAST search: not hits found)
  • If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
  • Processes running on the CLC Science Server will notify when they are done.
• Possibility to open results by clicking the button next to the process
• Possibility to find and select results in the Navigation Area by clicking the button next to the process
• You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)

3D editor re-design

• The 3D editor now allows you to select individual structure subunits, residues, active sites, disulfide bridges and even atoms, and to customize their appearance

General improvements

• Limited mode: when using a license server – if there are no more licenses left, you can still access your data. The Workbench will then run in Limited mode where only a few tools are available (corresponds to the tools found in CLC Sequence Viewer). Click “Limited Mode” in the license dialog.
• Tables:
  • New advanced filter to use numerical data for filtering and to combined several filter criteria. Click the small button next to the normal filter to see the advanced filter.
  • Visual feedback when sorting and filtering tables
  • Improved automatic detection of column width
• Performance of graphs and plots improved
• Local BLAST is upgraded to use NCBI BLAST version 2.2.19
• More elaborate error reports including error logs
• You can specify which folder the Workbench should use for temporary files
• Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
• The “Find” option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.

Plugins

• Extract Annotations plug-in has been improved:
  • Possibility to specify the naming of the sequences (based on annotation name, type etc)
  • Performance improvements to make it possible to extract annotations of large genomes.
• MLST plug-in: various bug fixes

Bug fixes

• Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer’s operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
• Fixed problem when BLASTing with an empty sequence
• Various performance improvements and bug fixes

The following has been updated

• The Side Panel’s Find only high-lighted the first hit. This is now fixed.
• Local BLAST: solved problem applying command-line parameters, now a checkbox determines whether command-line options should take effect
• BLAST: it was possible to use a BLAST result as input and database
• Trace data: fixed an error when deleting parts of an unsaved sequence with traces
• Better performance when zooming a dot plot
• Better performance when using the Side Panel’s Find in large contigs and sequence lists
• When right-clicking a CDS annotation and translating into protein, gaps were erroneously introduced into the protein sequence
• There was an error related to selecting sequences in the Cloning editor
• Multi-select (using Ctrl / Command key) did not work for sequence lists
• Various bug fixes

The following has been updated

• Fixed problems when scrolling very large sequences
• Fixed problem when importing very large GenBank files
• Improved possibilities for navigating contigs

New features

General performance improvements

• Improved performance when handling large data sets

Import and export

• Contigs can be exported in ACE format
• Export of graph data points in csv format

Various high-throughput sequencing improvements

• Possibility to open consensus sequence with gaps. Right-click the label of the consensus sequence in the contig view and select: Open Copy of Sequence Including Gaps. The gaps will be represented by Ns in the new sequence.
• Dynamic consensus graph removed from contig view. Since contigs now have a “real” consensus sequence which is also updated to reflect changes in the reads, the dynamic consensus sequence which is switched on in the Side Panel has been removed.
• Annotations can be transferred from reference to consensus sequence in bulk. Right-click one of the annotations and choose “Copy to Consensus Sequence” or “Copy Annotations of Type xx to Consensus Sequence”.

Plug-in updates

• New plug-in! GFF/GTF support: You can now annotate a sequence using a GFF/GTF file. The plug-in is available for all Workbenches (not CLC Sequence Viewer). Once installed, you find it in Toolbox->General Sequence Analysis-> Annotate from GFF/GTF File. Read more…
• Extract annotations plug-in updated: it now uses the name of the annotation as the name of the new sequence.

Bug fixes

• Fixed bugs related to contig editing.
• Various bug-fixes.

New features

• Scrollbars can be adjusted manually

Problems fixed

• Fixed problems when aligning sequences with lowercase characters
• Fixed import of trace files without quality scores
• Fixed problem when removing location
• A new sequence list can be created from a selection in the table view
• Better memory handling and managment of large contigs
• User definable scrollbar areas for contig views
• A few other minor bugs have been fixed.

Performance improvements

• Support for data handling for larger sequence lists
• Import of larger sequence lists (fasta)
• View larger sequence lists
• Sequence views with annotations are rendered much faster

Licensing system

• More smooth system for handling licenses based on license order IDs
• Support for download of a license via web interface
• License server support for plug-ins
• User-friendly license wizard
• More reliable license system
• Easier to upgrade to newer versions

Tables

• Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)
• Number of selected rows in a table is now shown in the status bar
• Enzyme lists and restriction site tables now includes information about the length of the recognition sequence of the enzyme
• Create a new sequence list from selected sequences in the sequence list table (right-click the selected sequences)
• Support for copying from an enzyme list and pasting into a spreadsheet
• Fine-grained filtering of specific columns in a table

Views

• Alignments: possible to batch delete sequences
• Alignments: possible to toggle marked status of sequences
• Shift-clicking to extend selection also works on sequences with restriction sites
• The mouse cursor’s position on the sequence is now shown in the status bar
• More fine-grained control when deleting annotations on multiple sequences
• Element info replaces the old “Sequence info” view and the “Properties” window. Undo-support and support for database-specific keywords.
• Improvement of scale layout of graphs

NCBI and UniProt search

• Results for searches includes information about the length of the sequence
• Ordering of search results makes it easier to add more results to the list

Assembly

• Assemble to Reference is now able to include both a consensus and a reference sequence in the same view
• There is a limit of max of 2000 sequence that can be assembled in one run
• Multiplexing:
  • Sort sequencing reads based on their name to facilitate batch runs
  • Sort sequences based on tag/barcode within the sequence
• Low coverage quick-find button in the Side Panel
• Advanced display of quality scores (colors/graph)
• Conflict table supports large contigs
• Coverage graph is shown per default
• Find Inconsistency renamed to Find Conflict
• Find Conflict treats gapped region as one conflict

Phylogenetics

• Advanced algorithm for Maximum Likelihood inference of phylogeny.
• ML estimation of model parameters on fixed phylogeny
• Substitution models included:
  • Jukes Cantor
  • Kimura 80
  • HKY
  • GTR

BLAST

• Local BLAST upgrade to 2.2.18
• NCBI BLAST uses the new server at NCBI
• The BLAST table includes information about the overlap

Miscellaneous

• Extract sequences works for large BLAST results, alignments, sequence lists and contigs
• Use an imported fasta file as motif list
• Better naming of primers when saving from primer table
• Motif search: the table now shows information about the length of a match
• Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)

CLC Combined Workbench 3.6.2

Release date: April 9, 2008

The following has been updated

• A few bugs resolved caused by the MLST plug-in
• BLAST of contigs no longer changes the contig name
• Fixed issue with tooltip rendering of quality values on reversed sequencing reads
• A few other minor bugs have been fixed.

CLC Combined Workbench 3.6.1

Release date: February 28, 2008

The following has been updated

• Various bug-fixes
• Fixed selection errors in cloning editor
• Name of saved primers were incorrect
• It is now possible to include NCBI BLAST in protein report
• Fixed copy/paste errors in sequence list table
• Made it possible to Ctrl-doubleclick to extend selection between restriction sites
• Improved user interface for adding motifs to motif lists

CLC Combined Workbench 3.6

Release date: February 6, 2008

The following has been updated

• Motif list search: It is now possible to do motif search using a list of motifs.
  • The list of motifs can be saved and exported
  • The list can contain different types of motifs: simple or regular expressions (Java or PROSITE)
• Multi request NCBI BLAST (up to 50 concurrent requests)
  • Makes it much faster to BLAST multiple sequences
  • Improved status messages when BLASTing multiple sequences
• Contigs (consensus sequence) fully supported by BLAST (both Local and NCBI)
• Extended BLAST table:
  • Shows if the hit is on the positive or negative strand
  • For tblastn, the reading frame for the hit is shown
  • The number of gaps, and gap percentage is shown
• BLAST overview table contains more information:
  • Shows hit with greatest percent identity
  • Shows hit with greatest percent positive
  • Shows longest hit
• Restriction sites available in Side Panel are computed up to 6 times faster
• Enzyme tables support “delete” via Tool bar and Delete key
• Enzymes already present in side panel are shown in [ ] brackets in “Show Enzymes Cutting Inside/outside Selection”
• It is now possible to reverse a sequence. Available both in the Toolbox under Nucleotide Analysis and in the right-click menu in the Cloning Editor.
• Better focus system – it is now easier to see what part of the screen that has focus. An error in the focus system has also been corrected.
• Various bug fixes.

CLC Combined Workbench 3.5.1

Release date: December 18, 2007

The following has been updated

• Organism name is now available in sequence list tables
• Fixed Mac problem when closing tabs
• Fixed minor issues and improved overall program stability
• Improved view layout of very long sequence labels
• Fixed stability issues related to the Recent Items plugin
• Improvement of a few issues regarding visualization of RNA structures on alignments

CLC Combined Workbench 3.5

Release date: December 06, 2007

Framework

• Search
  • Full text search (quick search field)
    • Query guide system (Shift + F1 in search field)
    • Pressing Alt while clicking: locate data in Navigation Area
  • Full text search editor
    • Can be saved for quick search later on
  • Automatically updated search index of all data
• New floating license concept
  • Automatic license server detection
  • Advanced license borrowing enables off-line use of workbench
• New and improved plug-in and resource management
  • New user interface
  • Quick button in toolbar
  • New concept: Resources – PFAM databases can be downloaded for easy update
  • Better progress measurement during download, installation etc.
  • Automatic update check
  • Integrated plug-in registration: SignalP, TMHMM, MLST
• Automatic restart (after plug-in installation, exceeding of memory capacity and license changes)

Views

• Cut, copy, paste and delete actions work better in both sequence viewers and tables (no need to right-click any more)
• Position of annotations in alignments, contigs etc. now relative to both alignment and sequence
• Numeric scales now shown on graphs along sequence (hydroplots, coverage, conservation, sequence logo etc)
• Selecting a row in a table makes an interactive selection on the corresponding sequence (now implemented for all relevant tables)
• The Find functionality in the Side Panel has been improved to make it possible to search in sequences with ambiguity character e.g. Ns
• It is possible to open much larger sequence lists in the graphical view.

Assembly

• Significantly faster algorithm now including multi processor technology – more than 4 times faster
• New action to reassemble contig
• Interactive mouse-adjustment of trimmed and excluded regions of sequence reads
• Refined conflict annotations now includes both existing and resolved conflicts
• Possibility to trim for multiple user defined vector sequences
• New action to reverse contig
• New right-click action to add sequences to an existing contig
• Sorting of contig reads (like alignments)
  • By hand (mouse)
  • By name
  • By length
  • By start position
• Individual scaling of trace data: mouse-grab the trace graph and drag up or down
• Possible to insert gaps in consensus sequence (Delete)
• Import of ACE files (e.g. contigs from Phrap)
• IUPAC codes included in the Contig table
• Editing sequence reads dynamically updates conflict annotations on consensus sequence (state: conflict or resolved)
• New right-click option on a consensus sequence selection: Transfer Selection to All Reads
• Trimming is performed twice as fast

Restriction sites

• Side Panel re-design
  • Sorting of enzymes by alphabet, number of cuts or overhang type
  • Simpler management of enzymes
  • Improved tool tips on side panel enzymes showing recognition sequence and cleavage pattern
  • Quickjump to restriction sites
• Improved enzyme selection wizard
• Improved action to Show Enzymes Cutting Inside/Outside Selection
  • New layout
  • Easier to understand
  • Improved filtering of enzymes cutting inside or outside the selection
  • Preview of enzymes to be added to the side panel
• Tool tips on restriction sites now include:
  • Methylation inhibition
  • Possible star activity (non-specific recognition and cleavage)
• Enzyme list table:
  • Information about possible star activity (non-specific recognition and cleavage)
  • New button: Add/Remove Enzymes
  • New button: Create new enzyme list from selection

Cloning

• Greatly improved wizard for in-silico cloning
  • Detailed table view of all available insert sequences
  • Interactive overhang “editor”: simple mouse interaction easily adjust sequence ends emulating exonuclease activity or Klenow fill
  • Graphically advanced compatibility aid and check of sequence ends
• Easily find enzymes with compatible ends
• Inserted fragments now include annotations with information about the parent sequence and the performed cloning steps
• Common cloning vectors now included in Example Data
• Naming of sequences in cloning editor now reflects the enzymes which have cut

BLAST

• Local “on-the-fly” BLAST (also Cube and Cell)
  • No need to build BLAST database aforehand
• Multi BLAST table – overview when blasting multiple input sequences(also Cube and Cell, NCBI BLAST, SNP BLAST)
• Possibility to use command line options in Local BLAST
• Hit length is shown in table view
• (Local) BLAST performance much improved for very large sequences

RNA

• Partition function calculation included
  • Calculates the complete secondary structure partition function.
  • Calculates the probabilities of all possible base pairs and the probability that any single base is unpaired.
  • Creates a plot of base pair probabilities.
  • The pairing probabilities are distinguished by color codes in both the linear- and the secondary structure editors.
• Structure scanning
  • Scan larger sequences for the existence of local stable RNA structures.
  • Creates a plot of structure formation probability. Statistical significance of a local structure can be seen as spikes in the graph.
• Hypothesis testing
  • Testing hypotheses about an RNA structure using added structural constraints
  • Probability assigned to hypothesis using the partition function
• Import and export of RNA secondary structures in different formats (ct / col / rnaml / xml).

Miscellaneous

• • Shuffle sequence includes more algorithms – now possible to shuffle while preserving di-nucleotide frequency
  • Added codon frequency tables for: *Arthrobacter aurescens TC1 *Streptomyces coelicolor A3(2)
  • Finding open reading frames: the table includes more information:
    • Strandedness
    • Nucleotides in the start codon
  • It is now possible to extract all sequences from a sequence list, an alignment or a contig (File->Extract Sequences)

Plug-ins

• Sequence reader – reads sequence aloud
• Recent items – show updated list of recently used data
• VNTI import – including import of VNTI archives

Example data

• Example data is included in the installation file – no need for download
• Large vector library included
• New RNA sequences

CLC Combined Workbench 3.0.3

Release date: October 04, 2007

The following has been updated

• Better import of aln files
• Solved problem with annotation rendering when inserting long sequences
• Annotation labels are now appended when exporting into GenBank format
• BLAST binaries are updated to version 2.2.17 which fixes some issues on the Windows platform
• Improved stability of the cloning editor
• Fixed problems with unstable contig objects

CLC Combined Workbench 3.0.2

Release date: August 22, 2007

The following has been updated

• BLAST databases are not indexed per default any more
• More information added to the BLAST output table
• Improvement of regular expression syntax in motif search
• Fixed error in contig editing
• A few help updates
• Better detection of memory on computers with more than 2 GB RAM
• Better license handling on Windows Vista
• Fixed error in alignment editing
• Improved program stability
• Improved ORF detection on negative strands of circular molecules
• Better file naming when importing raw sequence data

CLC Combined Workbench 3.0.1

Release date: July 5, 2007

The following has been updated

• Better handling of PFAM databases
• Fixed error in conversion of old sequence data with lowercase characters
• Old data can now be converted through the help menu
• Fixed error when trying to save an element to non-selected location
• A few help updates
• Better license handling on Windows Vista
• Fixed error in alignment editing

CLC Combined Workbench 3.0

Release date: June 28, 2007

The following has been updated

• Highlights
  • All the features of the CLC RNA Workbench are now included.
    • Algorithms for free energy minimization based prediction of RNA secondary structure
    • Advanced and fully integrated graphical editors for linear and 2D viewing and editing of RNA secondary structures.
    • Advanced prediction of secondary structure using predefined constraints for base pairing.
    • Table showing multiple secondary structures for one sequence
    • Overview of each structure element’s energy contribution
  • Work directly on data on a shared network drive
  • Improvements of annotation editing through the new annotation table.
  • Copy and paste annotations from one sequence to another.
  • New fragment table when doing restriction sites analysis.
  • Secondary peak calling
  • Translation of sequences in a contig improved (reading frames are aligned with consensus sequence, mutations on the amino acid level are shown in red – silent mutations are shown in yellow)
  • New scales for graphs along the sequence (in the Side Panel when viewing protein sequences under “Protein Info”):
    • Surface probability (Emini)
    • Backbone chain flexibility (Karplus and Schulz)
  • It is now possible to create a virtual gel simulating a restriction enzyme digest.
  • PFAM domains now include a link to the PFAM website providing more detail about the domain. The link is available from the Annotation table.
  • Full support for Windows Vista
  • One-click switch between views (e.g. circular and linear sequences views)
  • New annotation table – easy overview and filtering of annotations
  • State-of-the-art layout of annotations
  • Better and more intuitive handling of files (you can now access the files directly on the file system)
  • It is now possible to “Save as”
  • Easily expand selections using the mouse
  • Improvements of restriction site analysis

All the details

• Data handling
  • It is possible to add new locations to the Navigation Area by clicking the “Add Location” icon in the small tool bar above the Navigation Area. This makes it possible to use any folder directly from within the Workbench. A folder on a shared network drive can also be used enabling sharing of data with other users.
  • If more than one user tries to edit the same file, the second user who tries to save changes will be notified that the file has been changed. This user is then encouraged to use the “Save As” instead.
• Restriction sites
  • New restriction map object created when doing restriction sites analysis.
    • Restriction maps can be viewed as either fragment tables or virtual gels.
    • Fragments in tables are displayed with graphical illustration of overhangs.
    • When more than one enzyme cut at the same position, fragments are colored red to indicate that the result might differ in an in vitro experiment.
• Sequence views
  • Possibility to specify own annotation types. The list of annotation types can now be expanded simply by typing the name of a new type.
  • The Edit/Add Annotation dialog has been improved to make it possible to enter more information about an annotation. Following the conventions of the GenBank format, you can now add a number of qualifier/key pairs.
  • You can add links to web sites on annotations. In the qualifier/key part of the annotation dialog, you can simply enter a URL (link) and it will be possible to click on the link in the annotation table and open a browser.
  • More intuitive to edit alignments. Deleting and inserting gaps is now done for the selected sequences only. Deleting part of the sequence now moves the position of the rest of the sequence (instead of introducing gaps)
  • For graphs along the sequence, you can now enter a custom window size. Previously it was restricted to a few options.
• BLAST
  • In sequence views, you can make a selection, right-click and “BLAST Selection” both against NCBI and a local database.
  • Selecting a row in the BLAST table make a corresponding selection in the graphical BLAST view
• Motif search
  • Regions with N’s are not searched when doing motif searches.
  • Selecting a motif in a motif search table will make a corresponding selection in the sequence view.
• Primer design
  • It is now possible to set a value for “Maximum pair end annealing” score
  • In alignment-based primer design, it is now possible to specify a “No primers here” region like in the single-sequence primer design. It is available in the right-click menu on a selection.
• Assembly and sequencing data analysis
  • It is now possible to assemble to a reference sequence with only one read.
  • You can now right-click the name of a sequence in a contig and delete the sequence.
  • Improvements of the contig table: conflicts are now kept in the table after they are resolved. A new field has been added to indicate status as “Resolved”.
  • Single-click editing of single bases is now also possible in normal sequence views (it was previously only possible in contigs).
  • Secondary peak calling. In the Toolbox under “Sequencing Data Analysis”, you find “Call Secondary Peak”. It looks at the peaks in the sequence and is able to detect a “peak within a peak”. This is useful when looking for heterozygous mutations.
• General use
  • One-click switch between views (e.g. circular and linear sequences views). There is a new row of buttons at the bottom of each view which you can click to switch the view. Pressing Ctrl (Command on Mac) while clicking creates a split view of the two.
  • Pressing Ctrl (Command on Mac) while rolling the scroll wheel of the mouse can now be used to zoom in and out (only possible for mice with scroll wheels).
  • Many right-click menu items have now icons to make it easier to navigate the menus.
  • Simplifying the task of creating a new sequence. Rarely-used elements like “Keywords” and “Comments” have been removed from the dialog, and the two steps have been merged into one.
  • You can now use I (inosine) in nucleotide sequences.
  • Better choices for the resolution of exported graphics.
• Sequence views
  • Easily expand selections using the mouse. When you have made a selection, place the mouse cursor on the edge of the selection, and you can now adjust the selection. This is also possible for each part of a multiselection.
  • Quick-jump to annotations. In the Side Panel under “Annotation types”, it is now possible to click a quick-jump button which lets you go directly to the annotation. This provides a very quick and easy way of browsing annotations.
  • The names of annotations are now repeated on each new line in a wrapped sequence view.
  • The user can now specify which symbol to use in an alignment consensus sequence in case of ambiguities.
  • In nucleotide sequence views, you can introduce a space for every three characters to visualize codons. In the Side Panel under “Sequence layout” there are now several options for “Spacing”: Every 10 residues, every 3 residues in three reading frames.
  • It is possible to search in text views. In the Side Panel, there now is a “Find” group where you can enter a text to search for.
  • You can now hide labels in sequence views. This is particularly convenient with long sequence names taking up a lot of space.
• Import and export
  • Pasting simple sequence text (like ATCGTACGTA) in the Navigation Area automatically creates a new sequence.
  • Import and export of view settings (the settings saved in the Side Panel). In the Preferences dialog (available from the Edit menu), in the “View preferences” you can now export and import the View settings.
  • All tables can be exported in a CSV format (semicolon-separated). When exporting sequences in this format, the annotations are exported.
• Restriction site analysis
  • “Restriction Sites Analysis” has been renamed to “Create Restriction Map” and the dialogs are more intuitive to use.
  • It is now possible to filter the list of enzymes to easily pick a specific enzyme.
  • It is easier to set the number of cut sites for the restriction enzymes to be displayed
  • When you open an enzyme list, you can select a number of enzymes, right-click and “Create New Enzyme List from Selection”. This makes it easy to create subsets of enzyme lists. Combined with the table’s filter, this makes it easy to extract e.g. restriction enzymes from a specific vendor.
• Data handling
  • Copy an element in the Navigation Area by dragging while pressing the Ctrl button (Command button on Mac)
  • Filter elements in the Navigation Area (to show e.g. only nucleotide sequences). The filter is available from the small tool bar above the Navigation Area.
  • When selecting elements for analysis, only the relevant elements are shown (e.g. only nucleotide sequences are visible when selecting sequences for Restriction Site Analysis).
  • When selecting elements for analyzes (in the select elements dialog), you can right-click a folder and add all the elements in that folder.
  • Possible to sort elements alphabetically
  • One-click renaming of elements. Simply click an element which is already selected, and you can type a new name directly.
  • Recycle bin is now visible and you can easily restore deleted elements simply by dragging to the desired folder.
  • In the File menu, there is a “Save As” menu item. It saves the opened element under a new name.
  • Easily collapse all folders in the Navigation Area by clicking the “Collapse All” icon in the small tool bar above the Navigation Area.
• Plug-ins and licenses
  • Plug-ins are now installed for all users of a computer.
  • Licenses also apply to all users of the computer.

CLC Combined Workbench 2.2.4

Release date: May 30, 2007

The following has been updated

• Import of VectorNTI database significantly improved
• Fixed a problem with SNP BLAST caused by a change at the NCBI server.
• Fixed error that occurred when trimming away user defined vector sequence.
• Fixed minor problem in displaying trace files of extremely poor quality.

CLC Combined Workbench 2.2.3

Release date: April 24, 2007

The following has been updated

• Better support for Windows Vista
• Improved import of Swiss-Prot files
• User can now select DNA or Protein sequence for Fasta import
• Fixed assembly problem when deleting reversed read
• Minor BLAST changes

CLC Combined Workbench 2.2.2

Release date: March 08, 2007

The following has been updated

• Improved import of GCG files
• Improved import of BLAST alias files
• Workbench starts correctly on AMD64 linux distributions
• Fixed error when upgrading preference settings
• Fixed error in motif search if the search string is more than 127 characters
• Better handling when searching very large BLAST databases
• Fixed focus problem preventing interaction with Side panel

CLC Combined Workbench 2.2.1

Release date: January 30, 2007

The following has been updated

• The list of available BLAST database has been updated
• Now it is possible to use multi-volume blast databases
• Fixed error when opening a selection of reversed reads in the contig editor.
• Fixed error when deleting single stranded regions in the cloning editor.
• Fixed error in the bugsubmission dialog when it was invoked by a workbench crash
• Fixed error in the preference panel when using empty BLAST url

CLC Combined Workbench 2.2

Release date: December 18, 2006

The following has been updated

• Possible to install and use plug-ins
• Possible to develop your own plug-ins using our Software Developer Kit
• Improved editing of trace data
• BLAST databases can now be defined by the user
• Possible to specify the amplicon length in standard PCR
• BLAST databases can now be defined by the user
• SignalP and TMHMM is now available through plug-ins
• Various bugfixes

CLC Combined Workbench 2.1

Release date: November 29, 2006

The following has been updated

• Automatic annotation of raw sequences with SNPs, DIPs and other types of small scale variations. Annotation is based on user-friendly BLAST against the dbSNP database
• Better secondary protein structure prediction
• Additional parameters have been included in melting temperature calculations (Primer design)
• Improved 3D viewing of molecules; among others including simultanious viewing of sequence structures in 2D and 3D
• Greatly enhanced web based BLAST. Longer sequences can be BLASTed, the graphical user interface is improved, and the subsequent handling of search results has been improved
• Automated design of primers and TaqMan probes
• Enhanced BLAST on local databases. The graphical user interface is improved, and the subsequent handling of search results has been improved significantly
• You can now save HMM models generated in the Pattern Discovery function (searching for unknown patterns) – this reduces time for future pattern discovery searched significantly
• Advanced and interactive view of four different kinds of pairwise sequence comparisons:
  • Gaps
  • Differences
  • Identity
  • Jukes Cantor distances

These improvements and changes have been made in CLC Free Workbench and CLC Combined Workbench:

• Greatly improved data import: Manual work is reduced significantly when importing large amounts of data; e.g, when shifting from old software to CLC-software
• Much better handling of very large sequences: Much less memory use makes the application smoother to work with
• Significantly better data handling makes actions like deletion of files and working with many files at a time much faster
• Inclusion of pre-defined style sheets for the preference panel
• Greatly improved export of graphics
• Greatly improved printing
• Greatly improved file handling (faster etc.)
• Greatly improved save-function. Among others the option of creating new folders from the save dialog
• Tables are now searchable
• All output of analyses can now be shown in table

CLC Combined Workbench 2.0.4

Release date: November 9, 2006

The following has been updated

• Fixed error with help-files

CLC Combined Workbench 2.0.3

Release date: November 7, 2006

The following has been updated

• Swiss-Prot parser can now download and handle files from the UniProt (9.0) release (updated file format)
• Swiss-Prot parser again handles multi-entry Swiss-Prot files
• Fixed error dialog on exit of the workbench if an external file is deleted while kept open in another program

CLC Combined Workbench 2.0.2

Release date: August 2, 2006

The following has been updated

• Fixed rare cases where doubleclicking annotations in an alignment resulted in a wrong selection
• Fixed dialog when stopping BLAST runs in the process area
• References to BLAST databases are updated due to changes on the NCBI server
• Corrected check for 3′ end heterogeneity when predicting specific reverse primers based on an alignment

CLC Combined Workbench 2.0.1

Release date: July 18, 2006

These improvements and changes have been implemented in CLC Combined Workbench:

• BLAST: Expectation values with decimals now works for all locales
• Nexus parser fully functional
• Tracefile import updated: Gaps are replaced with wildcards
• Bootstrap values visible bug fixed
• Alignment gap-cost overflow management
• Cut/delete in navigator improved
• Even more user-friendly import-dialog
• Atom-count in sequence statistics bug fixed
• Bug fixed when downloading BLAST hit from graphical BLAST output viewer
• Attempting to drag more than 100 sequences no longer opens viewers
• Improved import of nucleotides from Vector NTI
• Import of oligos from Vector NTI

CLC Combined Workbench 2.0

Release date: July 6, 2006

All improvements below have been implemented in CLC Combined Workbench:

Improvements in CLC Free Workbench and all other Workbenches:

• All icons have been updated in order to support a more modern and platform-independent look
• Two or more sequences can now be joined into one
• Two or more alignments can now be joined into one
• The history log has been improved, giving an even better overview of past work tasks performed on a given element (an alignment, a sequence etc.)
• In order to give a better overview of sequences, they are now wrapped to fit the screen as default when they are opened.
• A large number of tool tips have been added
• All analyses have now an initial pre-defined setting of parameters. These parameters can be re-applied by the user’s choice
• Position specific information (e.g. the conservation score on an alignment) on sequences and graphs is now available by pointing to or selecting a position.
• DNA Strider data and PIR data can now also be exported (earlier only import was available)
• Import/export of NEXUS data
• Import of sequences in Staden format

Improvements in CLC Gene Workbench and CLC Protein Workbench:

• BLAST output can now be viewed in a table format, giving an easy overview of the data
• BLAST can now be performed on local databases
• You can now build local BLAST databases
• Motif searches can now be performed by using regular expressions
• Motif searches can now be performed by using ProSite patterns

Improvements in CLC Protein Workbench:

• The 3D viewer has been improved in several ways:
  • Better parsing of PDB data
  • Integration with the 2D sequence viewer
  • Implementation of tooltips on atoms
  • The BLAST of PDB data has been improved
• The Protein report has been improved significantly and now also includes
  • Signal peptide prediction
  • Secondary structure prediction
  • Transmembrane Helix prediction
  • PFAM search results

Improvements in CLC Gene Workbench:

Primer design

• Advance analysis of primer properties
• Alignment based primer design
• Alignment based TaqMan probe design

Assembly of sequencing data

• Option of aligning DNA sequencing data to an existing contig. This is especially useful when sequencing multiple exons from the same gene
• Tabular view of an assembled contig, including variance information. This provides an easy overview of conflicts in the data
• Improved “Assemble to reference sequence” functionality
• Option of finding inconsistencies
• Trimming annotation information is now included

Molecular Cloning and cutting

• The program now includes a fully integrated 1D DNA Gel Simulator
• The molecular cloning functionality has been improved

CLC Combined Workbench 1.0.2

Release date: April 19, 2006

All improvements and error fixing described below are implemented in CLC Combined Workbench.
These improvements and changes have been made to CLC Free Workbench and all other Workbenches

• The phylogenetic tree function has been improved: The number of replicates (the bootstrap value) is no longer fixed at 100. Any value can now be chosen.
• It is now possible to cancel the process when exporting views to graphics file formats such as .jpg, .pdf, and .svg etc.
• It is now possible to cancel “license upgrade” from within the program (Help menu)
• When sequences are opened, they are now zoomed to nucleotide level per default. The prior default setting was “fit to width”.

These errors and problems have been fixed in CLC Free Workbench and all other Workbenches

• Restriction site analysis: In some situations, updating from an older version of CLC Free Workbench to CLC Gene Workbench, CLC Combined Workbench, or CLC Free Workbench 2.5 or 2.5.1, resulted in the program freezing when selecting restriction enzymes. This problem has been fixed.
• Export of GenBank search parameters did not always work perfectly. This is now fixed.
• Running different types of CLC Workbenches right after each other could result in errors in some situations. This is now fixed.
• The user is now told if no hits were found in a database search – e.g. a GenBank search.
• Help-description in the programs: Users having an older version of JavaHelp installed than JavaHelp 2.0 did sometimes experience missing or in-optimal help-texts. This is now fixed.
• In a few situations, import of ABI files was not done correctly. This is now fixed.
• In some situations, resizing of the application changed the toolbar layout. This is now fixed.
• Naming a workspace with the same name as an existing workspace can now be done without problems.

In CLC Gene Workbench, this has been changed

• View of trace data: If ”View of protein-translation” is chosen, the amino acids are now located between the sequence and the trace data graphs. This gives a better overview of the translations.

In CLC Protein Workbench, this has been changed

• The Java 3D program extension is needed in order to view protein-molecules in 3D. Java 3D is however not installed as standard on Mac OS X 10.3.x. A warning is now given if this extension is not present on your computer.