This version is currently in beta.
Information about licensing beta products.
Improvements and new features
- The Roche 454 and SOLiD Import tools have been moved to the Legacy folder of the Workbench Toolbox. These will be retired in a future release.
- The option “Search on both strands” has been removed in the Trim Reads tool (formerly named Trim Sequences) and the Extract and Count tool.
- The Create Mapping Graph tool has been modified so that the coverage of overlapping paired end reads is now only counted as one in the overlapping region, instead of two as done previously.
- The SAM and BAM Mapping Files importer now fails if there are reads with more than one primary alignment where both are marked as being the first in a pair or both are marked as being second in a pair.
- Scrolling in a table now scrolls a fixed number of pixels, and not a fixed number of rows or columns.
- The “Adapter trimming” section of the Workbench Preferences has been removed. This section supported functionality that was already retired.
- The “Help” and “Reset” buttons in pop-up dialogs are now buttons with text labels. They were previously buttons with icons.
- Fixed an issue with the QC for Target Sequencing tool where “GC %” was reported as a ratio. It is now reported as a percentage.
- Fixed an issue where paired distances were calculated incorrectly for paired reads in Forward-Reverse orientation where there is adapter read-through. Paired distances can be seen in the report from the Map Reads to Reference tool and the RNA-Seq Analysis tool. The paired distance calculation is also used by the “auto-detect paired distances” option in these tools, although this issue is unlikely to affect the inferred distances.
- Fixed an issue with the Add Information about Amino Acid Changes tool when used with a circular sequence with a CDS annotation placed across the origin. Variants outside such a wrapped annotation could previously be incorrectly annotated with coding region changes.
- Fixed an issue with the Add Information about Amino Acid Changes tool when used with a circular sequence with an intron across the origin. Previously, nearby variants were not annotated with coding region changes. Now, variants in such introns and that are within 2 nucleotides of the nearest exon will be annotated with coding region changes, if such changes are identified.
- Fixed a bug in the RNA-Seq Analysis tool where, when run in “Genes and transcripts” mode, and using “Total counts” as Expression value, the expression values reported for GE tracks would not include shared exon counts. Downstream analyses based on the Set Up Experiment tool could be affected by this issue. Using affected GE tracks as input to the following tools would *not* affect their results: Differential Expression for RNA-Seq, Create Heat Map for RNA-Seq and PCA for RNA-Seq.
- Fixed an issue where the option to run the Differential Expression for RNA-Seq tool in batch mode was made available, leading to an error if it was selected.
- Fixed an issue where it was possible to start the Create Heat Map for RNA-Seq tool with invalid parameters that would cause the tool to fail.
- Fixed an issue where the number of input samples to the Map Reads to References and Map Reads to Contigs tools would be silently limited to 120. The execution is now aborted with a warning message. Each analysis must be started with 120 samples maximum.
- Fixed an issue with the mapping tool in the Workbench, which is used in tools involving a mapping stage, such as Map Reads to References, Map Reads to Contigs and RNA-Seq Analysis, where length and similarity fraction cut-offs in some cases were ignored for reads longer than 500bp.
- Fixed an issue with the InDels and Structural Variants that caused it to crash if it encountered a particular set of conditions relating to reads with deletions.
- Fixed an issues with the InDels and Structural Variants tool duplicate breakpoints and variants were reported if reads mapping as broken pairs were included in the analysis.
- 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.
- An issue has been fixed so that it is now possible to export in BAM format reads that contain synonyms, for instance ‘X’ as synonym for ‘N’.
- Fixed bug which caused the fasta exporter to fail when exporting read mappings where one or more reference sequences have no reads mapped to it.
- Fixed an issue that could cause exports of reports with line graphs to fail.
- Fixed an issue where resetting the default parameter values when configuring the Identify Candidate Variants tool did not work.
- Fixed an issue that would prevent the Trim Sequences tool being run with certain length filter settings.
- Fixed an issue where the option to “Highlight reverse paired reads” in the side panel of a reads track would cause paired end reads to be colored incorrectly if the reads completely overlapped, as would happen in the case of adapter read-through.
- 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.
- Fixed an issue where the Low Frequency Variant Detection tool could return NaN for the Probability value in rare instances for small datasets.
- Improved performance for several tools when handling genomes with many chromosomes. Examples include Add Fold Changes, Add Information from Overlapping Variants and the BED Exporter.
- 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.
The NGS import tools for Roche 454 and SOLiD will be retired in a future release of the software.