CLC Genomics Workbench versions

v9.0 [Feb 27, 2016]
Fixed an issue with the RNA-Seq Analysis tool that could arise when the "Genomes annotated with genes and transcripts" option was chosen: If two or more genes had the same name, and a transcript could be assigned to each from the mRNA track, then the value in the "Transcripts annotated" column in the GE track and in the TE track was 0. Furthermore, all counts for such genes were reported as zero, even when there were reads mapping to them.
Fixed an issue that arose when executing workflows with multiple inputs in batch, where changes to pre-defined, fixed inputs specified during the launch process were not applied.
Fixed an exception in the Read Mapping Editor that could arise when working with mappings to circular references.
Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
Fixed an issue where sorting a folder while saving into it could trigger an error.
Fixed a bug in the batch mode dialog that would lead to an error when problems related to the underlying file or data location were encountered.
Fixed broken help link in Ion Torrent importer.

v8.5 [Sep 14, 2015]
CLC Genomics Workbench 8.5
Release date: September 8, 2015
New features and improvements
The Sequencing QC report now contains the total number of reads in the summary.
Numerical comparison operators => and <= have been added to the filter tool for tables.
Quality scores ( QUAL ) are now calculated and added as annotations for variants. These values are included in VCF exports.
Batching on selected elements is now possible: it used to be restricted to selected folders.
The Search for Sequences at NCBI tool now has an option to search the EST database.
Improved memory management when handling large report elements.
Improved use of multiple cores when running the Create Detailed Mapping Report.
Improved use of multiple cores in the InDels and Structural Variants tool.
The output of the Reverse Complement Sequence now gets the suffix "-RC" attached to the name of the input. It used to be "-1".
The Hierarchical Clustering of Samples tool can now be executed as part of a workflow and can be executed on a CLC Genomics Server.
The fastq exporter can now export sequences up to 500Kbp. The limit used to be 32Kbp.
Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
Numbers are no longer appended to the names of Workflow elements when creating a copy of a Workflow using "Open Copy of Workflow".
Metadata Management. Keep track of input files and import meta information for your samples.
Changes
The tool "ChIP-Seq Analysis" has been renamed to "Transcription Factor ChIP-Seq"
Bug fixes
Fixed a SOLiD NGS importer bug where import of very low quality, colorspace-encoded, paired-end sequence reads in fastq format could lead to paired sequence lists where the wrong reads were marked as pairs.
Fixed an issue with the Map Reads to Contigs tool that could be extremely slow when included in workflows with multiple inputs.
Fixed a bug in the Annotate and Merge Counts tool where the Feature ID of mature 3' small RNAs in the "grouped on mature" tables was incorrect if the input data type was an Experiment.
Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
Fixed automatically generated link to COSMIC website, which previously led to retired page.
Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
Fixed an issue whereby Create Box Plot and Principal Component Analysis could sometimes be run with illegal arguments, leading to an error message.
Fixed a bug in the Predict Secondary Structure tool when the option to calculate the partition function was selected for long molecules (>1000 nucleotides).
Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
Fixed errors which prevent the side panel options of the gel view of a sequence list to be correctly applied and stored.
The list of Illumina adapters sequences has been removed from the Genomics Workbench.
Fixed an issue where one could not zoom in after zooming out fully on very large workflows.ing out fully on very large workflows.
Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.
Fixed exported reports having the wrong author in certain situations.

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.

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.