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QIAGEN CLC Main Workbench features

All CLC Main Workbench features are also included in CLC Genomics Workbench and CLC Genomics Workbench Premium 

Primer design

Primer design tools support the design of oligonucleotides – often referred to as oligos or primers.
As a user, you can define several criteria for primer design. When you adjust settings and parameters, both the primer calculations and the output of the calculations dynamically update. The program thus offers full interactivity in the dynamic search for the best primers.
The Workbench supports the design of standard and nested PCR primers and TaqMan probes, as well as sequencing primers and designs based on multiple sequence alignments.

Sanger sequencing data analysis

DNA sequence reads from Sanger sequencing machines (in file formats .SCF, .ABI or .PHD files) can be imported to the Workbench, trimmed and mapped to a reference sequence or assembled into contigs without use of a reference sequence. The tools can easily be combined in workflows for automation.

Interested in assembly of NGS or other high-throughput sequencing data? Get an overview of QIAGEN CLC Genomics Workbench.

Nucleotides that differ from the contig are colored, providing an overview of inconsistencies. A ‘Find Inconsistency’ option allows quick and easy inspection of called variants.

Traces, trimmed ends, coverage etc can be displayed for each contig and annotations, such as SNP annotations, can be added to regions of interest during the assembling process.

The Workbenches can also detect secondary peaks in Sanger sequence chromatograms – a peak within a peak – to help discover heterozygous mutations. Looking at the height of the peak below the top peak, the Workbench considers all positions in a sequence, and if a peak is higher than the threshold set by the user, it will be “called”.

Due to the integrated nature of the QIAGEN CLC Workbench it is easy to use the created contig-sequence as input for additional analyses such as BLAST analysis or cloning experiments.


Some of the many advantages of our contig assembly framework are:

  • Customized graphical display of trace data and quality scores
  • Automatic annotation of reference sequences with known SNPs from the dbSNP database
  • An integrated framework allows the use of sequence annotation (such as SNP information) to guide the interpretation of assembly results
  • Manual trimming or Automatic trimming of sequence reads based on quality scores, ambiguity characters and vector contamination
  • Graphical illustration of read coverage for an easy overview of contig confidence


QIAGEN CLC Main Workbench and QIAGEN CLC Genomics Workbench offer in silico cloning, design of vectors for various purposes and tools to perform in silico homology (Gibson) cloning, restriction cloning and Gateway cloning, including Multi-site Gateway cloning.

You can easily import from other formats, e.g., VectorNTI sequences and databases, to have all your cloning experiments in one site.

Advantages of our molecular cloning tools are:

  • A graphically illustrated cloning process with total user control
  • Sequence detail functionality allows easy overview of all fragment ends and overhangs.
  • Highly flexible mouse-controlled DNA manipulation to accommodate all forms of restriction enzyme, exonuclease and ligase activity
  • The option of introducing PCR fragments in the cloning process that are generated by the Primer Designer function, and have primer locations marked as annotation
  • All manipulations of sequences are done manually, giving you total control over how the sequence is constructed

Expression analysis

QIAGEN CLC Main Workbench and QIAGEN CLC Genomics Workbench can analyze expression data produced on microarray platforms. In addition, QIAGEN CLC Genomics Workbench can analyze next-generation sequencing data.

The Workbenches provide tools for performing quality control of the data, transformation and normalization, statistical analysis to measure differential expression and annotation-based tests. A number of visualization tools, such as volcano plots, MA plots, scatter plots, box plots and heat maps aid interpretation of the results.

Some of the features are:

  • Support for both microarray- and sequencing-based (post-mapping RNA-Seq) expression data
  • Interactive heat map and scatter plots for visualization
  • Transformation and normalization tools
  • Quality control tools, including principal component analysis, MA- and box plots
  • 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)
  • 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)


Multiple Sequence Alignment: All QIAGEN CLC workbenches include pairwise and multiple alignments of DNA, RNA and protein sequences.

The Additional Alignments plugin allows for use of ClustalW and Muscle.

The Whole Genome Alignment plugin enables the comparative sequence analysis of whole genomes and includes dot plot generation, alignment of multiple genomes, calculating average nucleotide identities, visualizing genomic relationships and extracting multiple sequence alignments for further processing.

Advanced alignment features include:

  • A number of alignment editing options
  • Joining alignments – can be used to construct “supergenes” for phylogenetic inference
  • Consensus sequence easily saved as a separate file for further analyses
  • Conservation of all sequence positions are shown below the alignment
  • Sequence logo displaying information content of all positions in the alignment
  • Transfer of annotations between sequences in alignments
  • Advanced pairwise comparison table for gaps, differences, distance and similarity

Other sequence analysis tools

Searching and retrieving sequences and vectors from NCBI and UniProt for use with QIAGEN CLC tools is easy.

Both Local and NCBI-based BLAST searches are supported.

General sequence analysis tools allow the manipulation of sequences, including annotation and extraction, Pattern discovery and Motif searches.  

Nucleotide analysis tools can reverse complement sequences, transcribe and translate sequences and find open reading frames (ORFs).

Protein analysis tools include calculations of charge, antigenicity, hydrophobicity, proteolytic cleavage and extinction coefficient, whereas Pfam domain search, signal peptide and transmembrane helix prediction allow annotation and characterization of proteins. In addition, tools for predicting secondary structures and homology modeling of 3D structures are available.

Reverse translation from amino acid sequence to DNA allows for codon optimization when constructing synthetic genes.

3D protein structure viewer

It is fast and intuitive to customize the visualization of molecules. The molecules are automatically sorted in categories; proteins, nucleic acids, ligands, cofactors and water molecules. A selection of visualization styles is readily accessible via quick-style buttons.

Proteins and nucleic acids can be visualized simultaneously in synchronized sequence and structure views, such that sequence annotation can be viewed in a 3D structural context.


QIAGEN CLC Main Workbench allows for the creation and visualization of phylogenetic trees and associated metadata. It is easy, for e.g., to find the optimal statistical approach by model testing and visualize imported metadata on tree topology, at high quality, ready for publication.

There are options to easily modify the tree layout and color scheme. Also, tools for generating phylogenetic trees using K-mer-based tree construction and for Maximum Likelihood analysis of amino acid alignments are available.


QIAGEN CLC Main Workbench offers an extendable toolbox through ready-to-use or tailored plugins.


Workflows are easily built in our Workbench and combine various tools from the toolbox into one analysis.

A workflow consists of a series of tools where the output of one tool is connected as the input to another tool.

Once the workflow is set up, it can be installed (either in your own Workbench, on a Server, or sent to a colleague) and you can then analyze many samples using the same standard pipeline with the same parameters with very few clicks.

Import from and export to

Import from and export to various standard sequence data formats is possible at any step in a workflow. In addition, results and figures can be exported as text, tables, in machine readable JSON format or in several standard Graphics formats.

Provenance and history

Each data element in QIAGEN CLC Main Workbench has its associated history.

The history information includes information on:

  • Date and time an analysis was run
  • Name version of the workflow and algorithms
  • Author of the analysis
  • Parameters and values set
  • Origin of the input data

The history can be Export in PDF or txt/JSON formats for use in electronic lab books or LIMS.