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.
v7.5 [Sep 2, 2014]
New features and improvements:
- "Filter Annotations on Name" can now insert names to filter on from significantly bigger files. Previously the limit for the file size was 10KB, this has now been increased to 20MB.
- RNA-Seq Analysis: The ENSEMBL gene id of each gene, where available, has been added as an additional column to the gene expression track output.
- Improved performances of the ChIP-seq Analysis tool for genomes with a large number of chromosomes.
- It is now possible to run a workflow without an optional input.
Bug fixes:
- A bug has been fixed in the Set Up Experiment tool. Exon-related expression values can now only be selected when present in the individual samples.
- When creating a subset of a paired experiment, the sub-experiment no longer appeared as being paired. This bug has been fixed and sub-experiments created in previous versions should recover the pairing information when accessed with this version of the workbench.
- 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.
- 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. Important: Please also check the description in the Gx 7.5 release notes of a bug fix in the translation of CDS annotations to protein sequences that was wrong in cases where the reading frame was not 1 or -1 in CDS annotations imported from ENSEMBL.
- Fixed problem importing VCF files using the AO and RO genotype field.
- Fixed problem importing certain VCF files.
- 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.
- Fixed problem with import of read mappings with supplementary alignments. When importing read mappings with supplementary alignments, supplementary alignments are not imported. Previously import of such read mappings caused import errors.
- Fixed rare problem with coverage that could occur in zoomed out reads tracks containing wrapped paired reads.
- Fixed rare error when sorting experiment tables.
- Fixed a bug in the Annotate and Merge Counts tool that in rare cases resulted in incorrect sorting and crash.
