CLC Genomics Workbench is a program that allows you to analyze, compare and visualize NGS data. The program uses a SIMD-accelerated assembly algorithm that can analyze high-throughput sequencing data faster. Also, it supports major next generation sequencing platforms, such as SOLiD, Ion Torrent, Complete Genomics, 454, and Illumina Genome Analyzer.
v7.0 [Feb 18, 2014]
Bug fixes:
- Fixed a bug in RNA-Seq Analysis regarding the calculation of RPKM. This error was introduced with the new RNA-Seq tool in CLC Genomics Workbench 7.0. When calculating RPKM, the total number of gene reads was used instead of total exon reads. This will only have a significant impact in case there are many intron reads mapped to this gene. With this release we have fixed the bug. Users that base their analyses on RPKM values conducted with CLC Genomics Workbench 7.0 - 7.0.3 should refer to our public notification about this issue to get further details, including how to determine if re-running RNA-seq analyses will be necessary and a work-around if this will not be possible. The Legacy RNA-Seq plugin is not affected by this bug.
- Fixed a bug in the Filter against Control Reads tool which meant that variants that are of type "Replacement" and which also introduce an insertion were not properly removed by the filter, even if there were reads supporting them. We recommend all customers that have relied on this tool for processing data with this tool in CLC Genomics Workbench 7.0.X to run the tool again in the 7.0.4 version.
- 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 bug that sometimes caused the workbench to crash when running "Local Realignment" on mappings generated with other mappers and imported as BAM files.
- Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow
Changes
- Users running RNA-seq analyses with only gene annotations can now choose whether to calculate the RPKM for these genes (i.e. genes without transcripts) or not.
