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.
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.
