Long Read Support plugin 24.0
Released on January 9, 2024
This release replaces the earlier beta versions of the plugin
New features and improvements
- New tool: Structural Variant Caller for Long Reads is capable of detecting structural variants with a length greater than or equal to 35 bp from long reads. The tool is based on Sniffles2 v2.2.
- De Novo Assemble Long Reads improvements:
- The tool now supports PacBio HiFi reads.
- The tool now supports assembly and reporting of contigs shorter than 10,000 bp. Previously, all contigs smaller than this were ignored.
- Map Long Reads to Reference introduces three read alignment options: Automatic, Automatic spliced, and Manual. With the two automatic options, read alignment parameters are set based on the sequencing technology that generated the reads. This improves mapping of in particular PacBio HiFi reads.
- RNA-Seq Analysis for Long Reads introduces two read alignment options: Automatic and Manual. With Automatic, mapping settings are based on the sequencing technology that generated the reads. This improves mapping of in particular PacBio HiFi reads.
- The version of Minimap2 has been upgraded to v2.26. This third-party code is used by the following tools, the output of which may consequently change: Map Long Reads to Reference, Correct Long Reads, and RNA-Seq Analysis for Long Reads.
- Correct Long Reads will reject PacBio HiFi reads as these are not supported.
- Template workflow De Novo Assemble Long Reads and Polish with Short Reads: a Trim Reads step has been added for the short reads input.
- For Create Sample Report, selected quality control metrics are supported for Map Long Reads to Reference and RNA-Seq Analysis for Long Reads.
- For Combine Reports and Create Sample Report, reports produced by Map Long Reads to Reference are now treated separately from those produced by Map Reads to Reference. The same applies to RNA-Seq Analysis for Long Reads versus RNA-Seq Analysis .
Bug fixes
- Fixed an issue causing reads mapped in reverse orientation with RNA-Seq Analysis for Long Reads to show up in the reads track as forward. The issue impacted visualization only. For RNA-Seq analysis reporting, reverse reads were correctly counted as such.
- Fixed an issue causing RNA-Seq Analysis for Long Reads to ignore user-specified values for “Maximum number of hits for a read” and instead always use the default value of 10.
