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QIAGEN CLC Genomics Workbench 11.0.2

Release date: 2018-12-06

Improvements

  • NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Reads in SRA, Search for Sequences at NCBI, Search for PDB Structures at NCBI 
  • The Search for Sequences in Uniprot tool now uses the HTTPS protocol.

Bug fixes

  • Fixed a bug where the "Unaligned end" field provided in the Breakpoint track output of the Indel and Structural Variants tool was left blank when the value should have been "Mixed consensus" on all but one chromosome. The field is now filled for all chromosomes.
  • Fixed a issue with the Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that caused a small minority of variants to go unreported under certain conditions expected to arise rarely.
  • Fixed an issue affecting the Map Reads to Reference tool when it was included in a workflow, where if the References parameter was connected to an input, and a masking track was configured, an error was reported stating that the masking track was incompatible with the reference genome, whether or not it was compatible. 
  • Fixed a bug in the Identify Candidate Variants tool where no results were returned when one or more criteria used a comparison operator with more than one term (e.g. ">=", "abs value <"). 
  • Specifying a reference cache size greater than 2GB was not possible when using a readmapper.properties file. 
  • Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again. 
  • Fixed the links to the AmiGO Gene Ontology website used for GO annotations. 
  • Fixed a bug where in some cases, the Search for Reads in SRA... tool would not fetch the final page of results.

Advanced notice

  • SOLiD colorspace data support, including import, is not available in the the next major release line of the software.
  • Roche 454 NGS import is now a legacy tool. We have retained it in the next major release line of the software, but it may be retired in a future release.

If you are concerned about these changes, please contact the QIAGEN Bioinformatics team (ts-bioinformatics@qiagen.com).



QIAGEN CLC Genomics Workbench 11.0.1

Release date: 2018-03-14

Improvements

  • Implemented the 3' HGVS compliance rule for c. annotation of variants: - When doing c. annotations (DNA-level HGVS) we annotate insertions that really are duplications as such. - For c. annotations we furthermore fulfill the 3' rule for insertions, deletions and duplications. - When determining amino acid changes, the 3' rule is applied to the DNA change first. This may shift a variant in or out of the coding region, and that will affect whether or not we consider it as an amino acid change.The 3' rule for p. annotations were previously fulfilled and are not affected by this fix.

Bug fixes

  • Fixed a bug in the VCF (Variant Calling Format) file format exporter that affected the QUAL score of the variant. Previously, the variant QUAL score was set to be the maximum QUAL score of all alleles (regardless of whether it was a reference allele or not). In some instances, e.g., when there are two alleles and one has poor QUAL score, this choice was suboptimal. Instead, the variant QUAL score is now chosen as the maximum QUAL scores among all non-reference variants.
  • Fixed an issue where the RNA-Seq Analysis tool would show an error if the first chromosome or contig contained no transcripts and the "Calculate expression for genes without transcripts" option was used.
  • Fixed an issue where the RNA-Seq Analysis tool would sometimes generate TE tracks that could not be used in downstream tools. The error occurred when the "Calculate expression for genes without transcripts" option was used on a gene track where two genes had the same name, one of the genes contained the other, and neither gene had a transcript.
  • Fixed an issue with the Trim Reads tool used in a workflow with multiple Trim adapter lists as input: all but the first list input were previously silently ignored, but the workflow now gives users a warning message.
  • Fixed an issue where importing a Trim Adapter List with an adapter with "Discard the read (end matches at 3')" was imported incorrectly.
  • Fixed an issue that could cause some third party plugins to fail trying to retrieve the fastq exporter.
  • Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
  • Fixed an issue with the advanced table filter functionality that prevented the removal of empty entries from columns expected to contain text.
  • Fixed an issue where Excel formatted files (.xls, .xlsx) could not be imported as Trim Adapter Lists.
  • Fixed a license issue causing workbenches to not start properly on Turkish Operating Systems.
  • Fixed issue causing the license assistant dialog and EULA dialog to be too big for smaller screens.
  • Fixed an issue where weblinks to Uniprot sequences led to the homepage.

Advanced notice

  • SOLiD colorspace data support, including import, will be retired and will not be available in the the next major release of the software.
  • Complete Genomics support, including import, will be retired and will not be available in the the next major release of the software.
  • Roche 454 NGS import is now a legacy tool. We plan to retain it in the next major release of the software, but it may be retired in a future release.

If you are concerned about the proposed changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).



QIAGEN CLC Genomics Workbench 11.0.0

Release date: 2017-11-21

Improvements and new features

  • Trim Reads:
    • The Trim Sequences tool under the NGS Core Tools section of the Toolbox has been renamed to Trim Reads.
    • A new option has been added to the Trim Reads tool: "Automatic read-through adapter trimming". This option makes it possible to automatically identify overlap in paired reads and will trim the region that is not part of that overlap. This option is turned on by default. This new default affects workflows that include Trim Reads (or by its former name: Trim Sequences); the parameter will be turned on and locked by default.
  • Trimming adaptor:
    • The New Trim Adapter List dialog has been updated to a new and more user-friendly interface.
    • It is now possible to reverse complement an adapter sequence with a "Reverse Complement" button to the right of the sequence field.
    • It is now possible to specify whether the trim should be performed on all reads, or only on the first or second read of a pair.
    • A visual shows the adapter and the sequence being trimmed in relation to the rest of the sequence depending on the option chosen when an adapter is found.
  • Fastq Export
    • Paired sequence lists can now be exported to 2 fastq formatted files, one file containing the first member of each pair, the other containing the second member. This is now the default for Fastq Export when exporting paired data.
    • The option "Output as single file" is now disabled by default.
    • The introduction of the new default setting "Export paired sequence lists to two files", has the implication that existing workflows that include a fastq export step will be in a state of conflict after they are updated for use on this release. This is because this option is not compatible with the option to "Output as single file", which was turned on by default in earlier versions. Affected workflows must be edited to either remove the option "Export paired sequence lists to two files" or the option "Output as single file". Messaging about this is provided when upgrading affected workflows.
  • RNA-Seq Analysis:
    • RPKM is now always calculated when running the RNA-Seq Analysis tool with the options "Genome annotated with genes only" and "One reference sequence per transcript".
    • The default for the reference type parameter is now "Genome annotated with genes and transcripts".
    • In the RNA-Seq Analysis tool, the option "Calculate RPKM for genes without transcripts" has been renamed to "Calculate expression for genes without transcripts".
    • The behavior of the RNA-Seq Analysis tool has been changed when the option “Genome annotated with genes and transcripts” is used together with the option “Calculate expression for genes without transcripts".
      • The counts of genes without transcripts are calculated. Previously only the TPM and RPKM were calculated.
      • For a gene without a corresponding transcript, where that gene is overlapped by the intron of another gene, reads aligning to this region are counted towards the expression of the gene without the transcript. Previously such reads were counted as belonging to the intronic region of the overlapping gene.
      • A single-exon transcript for each gene without transcripts is now added to the output TE track.
 
  • Workbenches without a license can now be run in Viewing Mode. In this mode, data can be viewed, imported and exported. Plugins needed for viewing certain data types can be installed. Viewing mode, with its added functionalities, replaces Limited Mode.
  • A dialog is now presented on startup if there are installed workflows that need to be updated before they can be run. The information about what to do to when a workflow needs to be updated has been improved.
  • The history of a data element can now be exported as a CSV format file.
  • The Extract Consensus Sequence tool can now be connected in a workflow to many more tools that take nucleotide data as inputs, including the Map Reads to Reference and Map Reads to Contigs tools.
  • An option to include reads that partially overlap variants has been added to the Identify Known Mutations from Sample Mappings tool, enabling detection of variants that are longer than the reads.
  • The Identify Known Mutations from Sample Mappings tool has been made slightly more strict when handling insertions and replacements, requiring reads to overlap adjacent reference positions to be counted as fully covering the variant.
  • The speed of the Illumina High-Throughput Sequencing Import has been substantially improved. The largest gains are seen on paired read files compressed by gzip with speed improvements of up to 30%.
  • Changed amino acids colors to better suit users with various forms of color blindness.
  • The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of QIAGEN CLC Genomics Workbench, so the version available for download could change over time from the one recorded here.
  • In table views, it is now possible to filter columns with the filters "Is in list" and "Is not in list" when the values are numbers.
  • When exporting files to SAM or BAM format files, information is now entered into the optional fields NM (edit distance) and MD (mismatch string).
  • The filter terms for the Identify Candidate Variants tool now include the numeric operators  '>=', '<=', 'abs value >=' and 'abs value <='.
  • Importing a GO annotation file with the Standard Import tool, specifying the format "Generic annotation file for expression data", now fails with an informative warning if any of the GO annotations are truncated.
  • Warnings are now reported if truncated GO annotations are found when opening data created by the Create Expression Browser tool.
  • The 'Expression Browser Table' (output from the  Create Expression Browser tool) now preserves sorting when changing the grouping, if sorting is not on any of the grouped columns.
  • NCBI blast executables are upgraded to version 2.6.0.
  • All wizard steps are now shown in the wizard sidebar when starting a tool or workflow.
  • Visualization of features that wrap around the origin of circular sequences has been improved for sequences and tracks.
  • Table filtering and search now interpret thousands and decimal separators in the same manner as the displayed table. Previously US punctuation was always used. This change means that if a table displays numbers in the form "123.456,7" then it is possible to find numbers less than ten by searching for "< 10,0" or "<10", but not "<10.0". If the table displays numbers in the form "123,456.7" then it is possible to find numbers less than ten by searching for "<10.0" and "<10", but not "<10,0".
  • When a tool is disabled in a right-click context menu, hovering the mouse over the tool name will now reveal why a tool was disabled in most cases.
  • The help window can now be closed by pressing the escape key.
  • The Download Reference Genome Data tool now downloads genome annotations from GFF3 files instead of previously as GTF files. Genome annotations for Homo sapiens versions hg18 and hg19 are still downloaded as GTF files, as these are not available as GFF3 files.
  • HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
  • This history information for data generated using the Identify Candidate Variants tool now  includes a match criteria field, recording if the option 'match all' or 'match any' was used.
  • For Reads tracks, the side panel option "Highlight reverse paired reads" is now enabled by default.
  • For stand-alone read mappings, read pairs with reverse orientation are now highlighted with a lighter blue color. This is identical to the 'Highlight reverse paired reads' option for reads tracks.
  • Parameters for the Trim Sequences tool are now shown in the same order when running the tool from the Toolbox or within a workflow.
  • The column headings in the table containing statistics for each mapping, optionally produced by the Create Detailed Mapping Report tool, have been made more descriptive.
  • The Search for Reads in SRA tool  now reports in the top left corner the number of rows being displayed.
  • Communication of error messages from the NCBI when running the Search for Reads in SRA tool has been improved.
  • Map Reads to Reference now outputs an empty read mapping and report when the input contains 0 reads.
  • A warning message is now presented when the tool Extract Sequences is run with the "Extract to single sequences option" selected and more than 100 sequences would result.

Changes

  • The Roche 454 and SOLiD Import tools have been moved to the Legacy folder of the Workbench Toolbox.
  • 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 Search for Sequences at NCBI tool now uses accession.version identifiers instead of GI numbers, as GI numbers are being phased out by NCBI (see https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/. )
  • 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.
  • Removed the line "Total consensus length" from Detailed Mapping Report when using a Read Mapping Track as input, as these tracks do not contain consensus information.
  • Clicking "Select genes in other views" in a Volcano Plot with an empty selection no longer gives an error message.
  • 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  Extract Consensus Sequence tool can no longer process protein BLAST results.
  •  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.
  • The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
  • The underlying read mapper and de novo binaries included in QIAGEN CLC Genomics Workbench 11.0 are from QIAGEN CLC Assembly Cell 5.0.5.

Bug fixes

  • Fixed an issue with the Create Statistics for Target Region 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 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 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 where the Amino Acid Changes tool would in some cases use the CDS reference instead of the RNA reference for annotating coding region changes. This would happen if the RNA and CDS annotations could not be matched, and it could cause variants in UTR regions to not be reported. The matching has now been improved by supporting the 'parent' field used by the GFF3 file format to pair CDS and RNA references.
  • 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.
  • Contigs with Gap annotations covering regions longer than 10 bp can now be successfully exported to AGP format. Sequences containing such gaps will be split into separate contigs on export. This issue will be particularly of interest to those using the Join Contigs tool of the QIAGEN CLC Genome Finishing Module.
  • 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 Annotate with Overlap Information, the BED Exporter, Filter Annotations On Name, and Motif Search.

Plugin Notes

  • 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.

Advanced notice

  • SOLiD colorspace data support, including import, will be retired and will not be available in the the next major release of the software.
  • Roche 454 NGS import has been moved to the Legacy Tools folder and will be removed in a future release, but will still be available in the next major release of the software.

If you are concerned about the proposed changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).



QIAGEN CLC Genomics Workbench 10.1.3

Release date: 2018-12-06

Improvements

  • NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Reads in SRA, Search for Sequences at NCBI, Search for PDB Structures at NCBI.
  • The Search for Sequences in Uniprot tool now uses the HTTPS protocol

Bug fixes

  • Fixed a bug where the "Unaligned end" field provided in the Breakpoint track output of the Indel and Structural Variants tool was left blank when the value should have been "Mixed consensus" on all but one chromosome. The field is now filled for all chromosomes. 
  • Fixed a issue with the Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that caused a small minority of variants to go unreported under certain conditions expected to arise rarely.
  • Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again.
  • Fixed the links to the AmiGO Gene Ontology website used for GO annotations. 
  • Fixed a bug where in some cases, the Search for Reads in SRA... tool would not fetch the final page of results.
  • Weblinks to UniProt sequences are now working again.
  • Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
  • Fixed an issue where the RNA-Seq Analysis tool would sometimes generate TE tracks that could not be used in downstream tools. The error occurred when the "Calculate expression for genes without transcripts" option was used on a gene track where two genes had the same name, one of the genes contained the other, and neither gene had a transcript.
  • Fixed an issue where the RNA-Seq Analysis tool would show an error if the first chromosome or contig contained no transcripts and the "Calculate expression for genes without transcripts" option was used.

Advanced notice

  • SOLiD colorspace data support, including import, will not be available from QIAGEN CLC Genomics Workbench 12.0 onwards.


QIAGEN CLC Genomics Workbench 10.1.2

Release date: 2017-12-05

Improvements and changes

RNA-seq analysis:
  • 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.
  • The behavior of the RNA-Seq Analysis tool has been changed when the option “Genome annotated with genes and transcripts” is used together with the option “Calculate expression for genes without transcripts".
      • The counts of genes without transcripts are calculated. Previously only the TPM and RPKM were calculated.
      • For a gene without a corresponding transcript, where that gene is overlapped by the intron of another gene, reads aligning to this region are counted towards the expression of the gene without the transcript. Previously such reads were counted as belonging to the intronic region of the overlapping gene.
      • A single-exon transcript for each gene without transcripts is now added to the output TE track.
General:
  • Fixed an issue where the number of input samples to the Map Reads to Reference tool 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.
  • Improved the information about what to do to when a workflow needs to be updated.

Bug fixes

  • 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 a bug in the Amino Acid Changes tool where the CDS reference was used instead of the RNA reference when annotating coding region changes if the RNA and CDS annotations could not be matched. This could result in variants in UTR regions not being reported. The matching has been improved by supporting the 'parent' field used by the GFF3 file format to pair CDS and RNA references.
  • 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 in the Add Information about Amino Acid Changes tool where the CDS reference was used instead of the RNA reference when annotating coding region changes if the RNA and CDS annotations could not be matched. This could result in variants in UTR regions not being reported. The matching has been improved by supporting the 'parent' field used by the GFF3 file format to pair CDS and RNA references.
  • Fixed a 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 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 issue where the Low Frequency Variant Detection tool could return NaN for the Probability value in rare instances for small datasets.
  • Various minor bugfixes

Advanced notice

Support for SOLiD colorspace data will be phased out over the next 12 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).



QIAGEN CLC Genomics Workbench 10.1.1

Release date: 2017-06-22

Genomics Workbench

Bug fixes

  • Fixed an issue introduced in QIAGEN CLC Genomics Workbench 9.5 causing the Merge Annotation Tracks tool to fail when used on tracks with more than 6 chromosomes.
  • Fixed an issue with the Cloning tool introduced in the QIAGEN CLC Genomics Workbench 10.1 where the tool could not be launched.

Advanced notice

  • Support for SOLiD colorspace data will be phased out over the next 18 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).


QIAGEN CLC Genomics Workbench 10.1.0

Release date: 2017-06-15

New features

  • Added keyboard shortcuts to change editor views. Ctrl + Shift + PageUp and Ctrl + Shift + PageDown now changes the current view of the currently focused editor.
  • New keyboard shortcuts are available for navigation within the workbench:
    • Navigate between open tabs with Ctrl + Page Down and Ctrl + Page Up (Windows/Linux/Mac). On laptops without Page Up/Down keys, the shortcuts are Ctrl+fn+arrow up/down.
    • Return focus to the navigation area with Alt + Home.
  • We have made the following improvements to tab presentation in the View area of the Workbench:
    • Tabs show more of the name of the opened object.
    • Tabs now open from the top left corner to the right and down.
    • Tabs always stay in the same position when another tab is selected or a new tab is opened.
    • A new sub menu has been added to the right click menu on tabs to select between the open tabs.
  • Anonymous Workbench usage information can now be shared with us to help us improve our products and offerings. Information about what is collected and how to opt out is provided when the updated Workbench is launched. Further details are available in the manual.

Improvements

  • New and improved Save View Settings dialog. This new dialog can be used for saving, applying, importing and exporting side panel views.
  • Improvement to the PCA plot generated by the PCA for RNA-Seq tool, so that all points are visible with default side panel view settings. Previously the standard view settings could hide points with missing metadata.
  • Stability improvements to SRA search:
    • Fixed an issue that could cause the SRA search to prematurely time out with the message "java.com.SocketTimeoutException".
    • Fixed an issue that could cause the SRA search view to display an error when trying to show results.
  • When importing tracks, the history of the track now contains the full path name of the imported file.
  • Opening large pairwise comparisons generated by the the Create Pairwise Comparison tool is now faster.
  • Improved messaging when installing workflows on a QIAGEN CLC Genomics Server from the Workbench.

Bug fixes

  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that could cause the count and frequency values to be too low for a small subset of those variants that are contained within a larger variant region (e.g. an MNV or deletion). For a variant to be affected by this problem, there needed to be at least two other potential variants nearby that were disregarded during the variant calling process. This circumstance and our testing suggest this is a rare issue.
  • Fixed a bug that in some cases would result in incorrect BaseQRankSum values being reported in the outputs of the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection tools.
  • Fixed an issue where switching to the Heat Map view on an Experiment would give an error when no Heat Map existed.
  • Fixed an issue where the GFF3 Exporter could generate invalid GFF3 for features of length 0.
  • Fixed a rare issue that could cause GenBank export to fail.
  • Fixed an issue with the Realign Selection tool where clicking on the ? button to see the manual information resulted in an error. This tool is launched from the right-click context menu for selections in sequence alignments.
  • Fixed an issue where workflows run in batch mode would fail in the case where no results are saved to the Navigation Area and only one file is exported per batch unit.
  • Fixed an issue introduced in QIAGEN CLC Genomics Workbench 10.0.1 where the Download Sequences from NCBI tool would continue to indicate it was searching when in fact the search had finished and no items were found.

Advanced notice

  • Support for SOLiD colorspace data will be phased out over the next 18 months.  If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).


QIAGEN CLC Genomics Workbench 10.0.1

Release date: 2017-03-15

Bug fixes

  • Fixed an issue where the Search for Sequences at NCBI tool did not display the first and last search result in each page of results returned.


QIAGEN CLC Genomics Workbench 10.0

Release date: 2017-03-02

New tools for RNA-Seq

  • Create Combined RNA-Seq Report - makes it possible to join multiple reports generated by the RNA-Seq Analysis tool into one combined overview report.
  • PCA for RNA-Seq*  - clusters samples in 2D or 3D. Known metadata about each sample is added as an overlay.
  • Differential Expression for RNA-Seq*  - uses multi-factorial statistics based on a negative binomial GLM.
  • Create Heat Map for RNA-Seq* - simultaneously clusters samples and features. Known metadata about each sample is added as an overlay.*
  • Create Expression Browser* - allows expression values, statistical results, and gene annotations to be viewed together.*
  • Create Venn Diagram for RNA-Seq* - shows differentially expressed genes shared between experimental conditions.*
  • Gene Set Test - tests the output from the Differential Expression for RNA-Seq tool for overrepresented gene sets (such as Gene Ontology terms) using a hypergeometric test.
  • Import | RNA Spike-ins - for importing RNA spike-in sequences and concentration data.
*Tools marked with an asterisk were available to earlier Workbench versions via the Advanced RNA-Seq plugin. They can now be found in the Toolbox in the RNA-Seq Analysis folder. These tools automatically account for differences due to sequencing depth, removing the need to normalize input data. They work with existing RNA-seq TE and GE tracks. Changes made in this release mean that outputs from the Differential Expression for RNA-Seq tool can now be used as inputs to the Extract Annotations and Extract Reads Based on Overlap tools.

RNA-Seq Analysis

  • The RNA-Seq Analysis tool now supports RNA spike-ins, such as ERCC and SIRV, for quality control. This makes it possible to validate RNA-Seq experiments by comparing known spike-in concentrations to measured transcript concentrations. Spike-ins can be imported using the new RNA Spike-ins Import tool.
  • The RNA-Seq Analysis report has been revised and updated:
    • We now show the distribution of the biotypes that the reads mapped to.
    • The strand specificity  of the mapped reads is now reported.
    • Transcript coverage plots make it possible to detect and visualize 5' and 3' coverage bias.
    • For paired-end reads, we now detect and warn about potential adapter read-through.
  • A biotype column is now available in the Expression Track tables produced by the RNA-Seq Analysis tool, when biotype information is available.
  • The Mapping options of the RNA-Seq Analysis tool, "Map to gene regions only" and "Also map to inter-genic regions", have been removed. The tool now runs by mapping reads to the full reference supplied, which is equivalent to choosing the recommended "Also map to inter-genic regions" option in earlier versions.
  • The RNA-Seq Analysis tool now always uses the "Expression level" option "Use EM estimation (recommended)" to quantify expression. This is more accurate than the previous default option. Differences are especially noticeable for Transcript Expression (TE) tracks.
  • The RNA-Seq Analysis quantification by EM estimation now runs faster.
  • In RNA-Seq analyses, reads that map uniquely to a genome position are now always marked as unique. Previously, a uniquely mapped read would be marked as ambiguous if it mapped to a position with multiple overlapping genes.
  • Exon IDs will no longer be included in the ENSEMBL column of transcript expression (TE) tracks generated by the RNA-Seq Analysis tool. Gene and transcript names will continue to be listed and hyperlinked in this column.

Import/Export

  • A tool to import PacBio data is now available at Import | PacBio.
  • Usability aspects of data association using the Import Metadata tool have been improved, including adding a preview of data items to be associated with particular metadata rows.
  • Fasta is now the default format the first time the Import | Tracks tool is invoked (was GFF2/GTF/GVF in earlier versions).
  • The GFF2/GTF/GVF tracks importer can no longer be used to import GFF3 format files. The new GFF3 tracks importer should be used for this instead.
  • The GFF3 importer has been updated with respect to the handling of CDS features. In earlier versions, CDSs with different IDs but the same parent gene would always be merged into the same CDS feature during import. This behavior will still occur in cases where all CDSs in the GFF3 file either have unique IDs or no IDs. For GFF3 files where there are any CDSs with identical IDs, then only CDSs with the same ID are merged into a single feature.
  • The Import | Tracks tool now accepts files with a .fna extension.
  • The display of the types of files to import using the Import | Tracks tool has been improved.
  • The speed of importing to tracks where the original file contains data relating to many chromosomes has been substantially improved.
  • RNA tracks imported from GFF3 format files are now colored according to their biotype.
  • The Cosmic option of  the Import | Tracks tool is now more flexible with regards to the column headings in the files being imported.
  • An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
  • An option has been added to create an index file when exporting to BAM format.

BLAST

The list of BLAST databases for use with the BLAST at NCBI tool has been updated:
  • Added “RefSeq representative genomes” database.
  • Removed “New or revised GenBank sequences (month)”. This is no longer supported by the NCBI.
  • Changed “References mRNA sequences”name to “References RNA sequences”. The database that is searched remains the same as before.
  • Changed “16S ribosomal RNA sequences” database to now search the  “rRNA_typestrains/prokaryotic_16S_ribosomal_RNA” database, as listed on the NCBI website. It previously queried “TL/16S_ribosomal_RNA_Bacteria_and_Archaea”.
  • Fixed “Human genomic plus transcripts” and “Mouse genomic plus transcripts” databases configuration to reflect their new location. Searching these previously returned an error.

New features and improvements

  • Toolbox rearrangement: the expression analysis tools are now in two top-level folders: "RNA-Seq Analysis" and "Microarray and Small RNA Analysis". The former top level Toolbox folder Transcriptomics Analysis has been removed.
  • When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms. This improvement affects the tools: Hypergeometric Tests on Annotations and Gene Set Enrichment Analysis (GSEA).  
  • 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 has been updated. The update includes improved read mapping quality and speed (especially for longer reads), improved memory performance for the index building stage, and various minor bug fixes. The new mapping tool corresponds to the clc_mapper tool included in Assembly Cell 5.0.3, planned for release in March, 2017.
  • The default value for the parameter "Maximum guidance-variant length" in the tool Local Realignment tool has been changed to 200 (was 100). This change applies to all ready-to-use workflows and when the tools is launched directly.
  • The Basic Variant Detection tool will no longer report N as an alternative allele when there is an ambiguous base at a variant position.
  • The report generated by the tool Create Statistics for Target Regions now includes a "≥" sign instead of a ">" sign.
  • The "Additional Reporting" options in the Create Sequencing QC Report tool,  "Quality analysis" and "Over-representation analysis" have been removed. These outputs are now generated by default.
  • A PubMed search option has been added to the Search for Reads in SRA tool. This returns only those runs that are associated with a PubMed abstract or full-text article.
  • Support has been added for 'negative lookahead' when using Java regular expressions when using the Motif Search Tool.
  • For new or existing sequence lists the sequencing platform can now be specified via the Read Group setting of the Element Info view.
  • It is now possible to right-click on a table cell and filter table rows based on the value of that cell by choosing options under the new context menu section called  "Table filters". This change applies to all tables where advanced filtering is available.
  • The speed of sorting and loading tracks has been greatly improved. Due to these changes, tracks created with this or later versions of the Workbench cannot be used with older Workbenches. Backwards compatibility has been maintained: tracks created using older versions of the Workbench can continue to be used.
  • The speed of searches for data elements with associations to specified metadata, from within a Metadata Table, has been greatly improved. To enable metadata related searches to work after upgrading to the QIAGEN CLC Genomics Workbench 10.0 indices for the locations containing the relevant data will need to be rebuilt.
  • Columns with position information in the table produced by Find Broken Pair Mates tool now sorts numerically rather than alphabetically. Alphabetic sorting for these columns was introduced with the QIAGEN CLC Genomics Workbench 9.0. Earlier versions had numerical sorting.
  • Tutorial windows are no longer blocked when a wizard is open.
  • Various minor improvements

Bug fixes and changes

  •  Fixed an issue where the index building stage of the Map Reads to References and the Map Reads to Contigs tools was not taking into account the maxcores setting in the cpu.properties file, where this had been configured.
  • Fixed an issue where sequence circularity was not reported in the output from the Map Reads to References tool.
  •  Fixed a bug in the Create Detailed Mapping Report tool, which sometimes reported incorrect read counts for circular sequences.
  • Fixed an issue where the Basic Variant Detection, Low Frequency Variant Detection and  Fixed Ploidy Variant Detection tools reported homozygous reference insertions in cases where a heterozygous variant was possible but the insertion variant was disregarded during filtering.
  • Fixed an issue where the Identify Known Mutations from Sample Mappings tool would fail if it was part of a workflow and it received multiple input sample mappings as input.
  • Fixed an issue with the Annotation Table view of a sequence where it was possible to change the types of annotations displayed at the same time as an annotation was being edited, which could lead to an error being thrown or the wrong annotation being changed.
  • Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
  • Fixed an issue with Primer Tables where an error resulted if either the option "Save Primer(s) Fwd, Rev" or "Save Fragment" was chosen and then the save operation was stopped by clicking on the Cancel button.
  • Fixed an issue where in some cases filtering tables for empty values would not produce any results.
  • Fixed an issue where advanced filtering did not work when looking for rows with cells containing multiple values using the filtering term "=" (equals).
  • Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
  • A sporadic java issue that led to errors including the text "java.lang.ClassCastException: sun.awt.image.BufImgSurfaceData cannot be cast to sun.java2d.xr.XRSurfaceData", has been addressed through an upgrade to java. This issue was primarily seen when using the Workbench remotely on Linux systems.
  • Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST or QIAGEN CLC Microbial Genomics Module installed.
  • Various minor bugfixes.

Retirement

  • The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.
  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools have been retired and have been removed from the Legacy folder of the Toolbox.
  • Tools in the Expression Profiling by Tags folder under the Toolbox | Legacy area have been retired and this folder has been removed. The tools retired are Extract and Count Tags, Create Virtual Tag List and Annotate Tag Experiment.

Plugin notes

  • The Advanced RNA-Seq plugin has been retired. The tools from this plugin have been integrated into the software. Please see the New Tools for RNA-Seq section for more details.

Other notifications

  • An option to opt out of providing anonymous usage information to QIAGEN has been added to the Workbench Preferences. We are not yet collecting any usage information so opting in or out does not have any effect at this time.


QIAGEN CLC Genomics Workbench 9.5.5

Release date: 2017-06-08

Improvements

  • When importing tracks, the history of the track now contains the full path name of the imported file.

Bug fixes

  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that could cause the count and frequency values to be too low for a small subset of those variants that are contained within a larger variant region (e.g., an MNV or deletion). For a variant to be affected by this problem, there needed to be at least two other potential variants nearby that were disregarded during the variant calling process. This circumstance and our testing suggest this is a rare issue.
  • Fixed a bug that in some cases would result in incorrect BaseQRankSum values being reported in the outputs of the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection
  • Fixed an issue that could cause the SRA search view to display an error when trying to show results.
  • Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected Workbenches with the CLC MLST or QIAGEN CLC Microbial Genomics Module installed.


QIAGEN CLC Genomics Workbench 9.5.4

Release date: 2017-02-14

Improvements

  • In cases where tools within a workflow have been renamed, it is now possible to filter for original tool names within the workflow configuration view of the workflow editing tool.

Bug fixes

  • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the QIAGEN CLC Genomics Workbench 9.5 has been extended to 7 weeks. The tools affected by this change are Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Filter Reference Variants, Identify Candidate Variants, Coverage Analysis, and InDels and Structural Variants.
  • Fixed an issue in the RNA-Seq Analysis tool where running in EM mode, with a "Strand specific" setting of "Forward" or "Reverse" would result in the second read of a pair mapped as a broken pair being counted incorrectly if that read was mapped outside a region annotated as a transcript.
  • Fixed an issue where an error arose when using the RNA-Seq Analysis tool with the EM option and a strand specific setting of "Forward" or "Reverse" in cases where the second read of mapped broken pair mapped to the opposite strand of the strand specific setting.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
  • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
  • Fixed an issue in the InDels and Structural Variants tool that would terminate analysis of large read mappings prematurely a fraction of the times.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
  • Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection, Low Frequent Variant Detection and Local Realignment tools could fail if a deletion was encountered at the end of a match between a read and the reference in the mapping used as input.
  • Fixed an issue in the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequent Variant Detection tools where the tools could stop with an error. The problem arose when a read split up within a mapping (e.g. to map to separate exons) was split into 4 or more parts, and at least 4 of those parts would map within a region of adjacent variants being considered as a possible multiple nucleotide variant (MNV). This infrequent problem was most likely to occur when using high coverage RNA-Seq mappings and looking for variants occurring at low frequency. It was introduced in the previous bugfix release of the QIAGEN CLC Genomics Workbench, version 9.5.3.

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in March 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in March 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com), letting them know the OS being used and the products you are running on that OS.
    • Windows: Windows Vista and Windows Server 2008
    • Mac: Mac OS X 10.7 and 10.8
    • Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21


QIAGEN CLC Genomics Workbench 9.5.3

Release date: 2016-12-14

Improvements

  • Server import and export locations shown in Workbench wizards now have tooltips giving the path to those locations.
  • Various other minor improvements (e.g. improved tooltips)

Bugfixes

For the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools, the following have been addressed:

  • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
  • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
  • Fixed an issue where, for an SNV without immediately adjacent variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
  • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.

The above issues, including information on the products affected, are described on the public notification page: Coverage and count reporting for variants in certain circumstances are incorrect

For the Identify Known Mutations from Sample Mappings tool, the following issues have been addressed:

  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where reads in a sample mapping were not identified as supporting the presence of a known variant in cases where the first position of the variant region in the mapped read contained a gap.
  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where a read containing a variant longer than a known variant being tested for was counted as supporting the known variant in cases where the first part of the read’s variant sequence is identical to that of the known variant.
  • Fixed an issue in the Identify Known Mutations from Sample Mappings tool where overlapping reads of a pair having conflicting base calls for a variant position could contribute to the coverage calculated for that variant.

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com), letting them know the OS being used and the products you are running on that OS.
    • Windows: Windows Vista and Windows Server 2008
    • Mac: Mac OS X 10.7 and 10.8
    • Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21
 


QIAGEN CLC Genomics Workbench 8.5.4

Release date: 2017-03-22

All changes in this release have also been fixed on the QIAGEN CLC Genomics Workbench 10.x and 9.5.x lines at time of writing, with the exception of the one release note marked with an asterisk. That issue was fixed for QIAGEN CLC Genomics Workbench 10.0 and will be fixed in a future  release from the QIAGEN CLC Genomics Workbench 9.5.x line.

Improvements

  • All NCBI server communication is now encrypted (uses HTTPS).
  • Updated the URL to use for links to UniProt databases.
  • Updated BLAST executables to be compatible with macOS Sierra. This change only affects Mac users.

Bug fixes

  • For the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection tools: 
    • Fixed an issue where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
    • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
    • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.
    • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
    • Fixed an issue where for a SNV without immediate neighboring variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
    • Fixed an issue where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
  • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
  • Fixed an issue where, when searching for both read1 and read2 in a broken pair, the Find Broken Pair Mates tool reported that the mate of read1 was itself. The tool now correctly shows that the mate of read1 is read2.
  • Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
  • Fixed a bug in the Manage Enzymes wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
  • Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected Workbenches with the CLC MLST Module or QIAGEN CLC Microbial Genomics Module installed.*


QIAGEN CLC Genomics Workbench 6.5

Release date: 2013-08-21

 

New features

  • Variant detection:
    • New tool for adjusting read mappings through local realignment. The Local Realignment tool has the option to realign unaligned ends, realignment with a guidance variant track (e.g. obtained from external resources such as dbSNP, through the Indels and Structural Variants tool described below or from analysis of other read mappings) and allows for realignment of multiple samples. Has previously been available as a beta plugin.
    • New tool for detecting structural variants (detects insertions and deletions, intra-chomosomal translocations, tandem duplications and inversions) working on "unaligned ends (soft clippings)". Has previously been available as a beta plugin.
    • Important changes to variant reporting: adjacent variants are now reported as one variant instead of linked variants.
    • A new variant filter has been added to both “Probabilistic Variant Detection” and “Quality-based Variant Detection”: “Ignore variants in non-specific regions”. This new filter ensures that variants in regions covered by just a few non-specific reads are ignored.
    • Probabilistic Variant Detection: A new threshold filter, “Required variant count”, has been added to the wizard. This filter ensures that only variants present in a number of reads that exceeds the specified threshold are called.
    • Quality-based Variant Detection: Addition of a new column that reports hyper-allelic status of variants. This is based on the specified threshold “Maximum expected allele” in the “Set genome information” wizard under “Ploidy”. The output in the table is “Yes” or “No” with respect to whether the threshold has been exceeded.
    • A new column has been added to the variant track table that describes the length of the insertions, deletions, and replacements. This makes it possible to filter on the length of e.g. insertions/deletions.
    • VCF export is now using genotype fields. The tag CLC AD is used for count of a variant, and PL is used for coverage. In this version, one variant track will result in one VCF file.
  • Variant annotation:
  • Workflows:
    • Automatic adjustment of layout in workflows. It is now (again) possible to adjust the connected workflow elements automatically. Right click in the workflow editor to access a menu with the option "Layout". Clicking on "Layout" will adjust the layout of the workflow. The layout can also be adjusted with the quick command Shift + Alt + L.
    • Automatic update of tools in workflows. Tools in existing workflows will automatically be updated when opened from the Navigation Area. If new parameters have been added to the updated version of the tool, these will be used with their default settings. A workflow can be kept in its original form by saving the updated workflow with a new name as this will ensure that the old workflow is kept rather than being overwritten.
    • Information: In the “Manage Workflows” dialog a new tab has been added providing information about the workflow (such as when it was built and which version of the workbench was used).
    • Highlight used elements: In the Side Panel under “View mode” it is now possible to select “Highlight used elements”, which will show all elements that are used in the workflow. Unused elements are grayed out. The “Highlight used elements” can also be activated with the quick command Alt+ Shift + U.
    • Highlight Subsequent Path: Is a further development of the old option “Mark Subsequent Path”.  If you right click on the name of one of the tools in a workflow, it is possible to select “Highlight Subsequent Path”, which will highlight the path in the workflow from the tool that was clicked on and further downstream.  All other elements in the workflow will be grayed out.
    • Create Installer: A workflow can now be installed directly from the workbench. This can be done with the “Create Installer” button (or the quick command Alt + Shift + I). Three options exist in the “Create Installer” dialog: 1) Install the workflow on your local computer, 2) Install the workflow on the current server (requires that you are logged on to the server and that you are the administrator), and 3) Create an installer file to install it on another computer.
    • Export can now be part of workflows.
    • Workflow enabled elements can be dragged directly from the Toolbox into the workflow editor.
    • Workflow images can be copied from the editor by using Ctrl + C (copy) and pasted into the desired destination with the Ctrl + V command.
    • All elements can be removed from the workflow with the shortcut Alt + Shift +R.
    • Previously, when running the “ChIP-Seq Analysis” tool, the result would be a copy of the read mapping with annotations added. Now the annotations are added to the read mapping used as input. Workflows using the "ChIP-Seq Analysis" tool must be manually updated, deleting the ChIP-Seq workflow element and adding it again.
    • Reinstallation of modified workflows can now be done directly with the “Create Installer” function. A pop-up dialog provides the option to make "forced import" of an already installed workflow.
    • Speed improvements in the workflow editor means that the user experience when editing large workflows has been greatly improved.
    • New tools that are now workflow-enabled:
 
  • 3D Molecule Viewing: The integrated viewer of structure files, the 3D Molecule Viewer, has been completely redesigned. The Molecule Viewer offers a range of tools for inspection and visualization of proteins and other molecules stored in structure files from the Protein Data Bank (PDB).
  • De novo assembly
    • New tool: Map Reads to Contigs. This tool allows mapping of reads to contigs. This can be relevant in situations where contigs have been imported from an external source,  the output from a de novo assembly is contigs with no read mapping, or if you wish to map a new set of reads or a subset of reads to the contigs. Scaffolds can be exported in AGP format: scaffolded contigs are exported as individual contigs and not as a single scaffold with N's inserted in between contigs. This allows for submission-ready data.
    • Great performance improvement when updating the contig sequence based on reads that are mapped back to contigs.
  • Tracks: Several new features have been added

It is now possible to:

    • When there are more reads than can be shown in the available view area, an overflow graph will be displayed below the reads. The overflow graph was previously shown in grey. Now the overflow graph is shown in the same colors as the sequences. Hence, it is now possible to distinguish forward, reverse and paired reads in the overflow graph as well as mismatches in reads.
    •  Insertions from variant tracks and reads tracks can now be shown in tracks.
      • For variant tracks, a new side-panel option “Insertion” allows the user to select whether to display insertions or not.
      • For reads tracks insertions seen in more than a given percentage of reads are shown. The default percentage is 1%, setting it to 0% will show all insertions (like the cluster editor) and setting it to 100% will show no insertions.
      • Insertions in reads tracks that are present at a frequency below the specified threshold are shown with a vertical line in the reads to indicate its location.
      • Reads tracks now also have a mouse-over tooltip that provides information about insertions at specific positions. This tooltip reports the number of reads that contain the insertion and lists what was inserted.
    • Extract reads from read tracks in two different ways:
  1. Extract sequences from tracks. Allows extraction of all reads as single sequences or as sequence lists.
  2. Extract from selection. Allows the creation of a reads track containing only reads that fall within the selected region, and of specific types.
    • Four new options are available in the Side Panel for Track layout when viewing a reads track:
      1. Show quality scores: Makes it possible to adjust the colors of the residues based on their quality scores. In cases where no quality scores are available, blue (the color normally used for residues with a low quality score) is used as default color for such residues.
      2. Matching residues as dots: Replaces matching residues with dots in reads tracks. This option makes it easier to spot variants.
      3. Show read type specific coverage: When enabled, the coverage graph that summarizes those reads that could not be explicitly shown is now replaced by one coverage graph for each read type found in the Reads track. This can be used for easy and visual comparison of the strand specific coverage.
      4. Only show coverage graph: When enabled, only the coverage graph is shown and no reads are shown.
    • A new tool has been included: “Identify Graph Threshold Areas”. This tool uses graph tracks as input to identify graph regions that fall within certain limits (thresholds that have been specified by the user).
    • Extract annotations from track. This tool makes it very easy to extract parts of a sequence (or several sequences) based on its annotations.
    • Create a track list with the shortcut  Ctrl + L
    • The create histogram tool now also accepts graph tracks as input.
    • The error message "Too much data for rendering. Either zoom in to view data, or adjust data aggregation threshold" has now been added to the big grey box that appears in cases where a track cannot be shown. Previously only a big grey box was shown with no further explanation.
    • Opening a large table view of a variant track is no longer blocking the user interface. It is running in the background, and it is possible to stop loading the data by closing the table view.
  • Export framework redesigned
    • Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
    • Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.
    • Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a  description of each exporter that can be quickly filtered.
    • Export can be integrated into workflows
    • Support for direct compression of exported files in zip and gzip.
    • Previously, VCF export required the user to know that both a variant track and a sequence track should be selected before exporting. This has changed, so that the user only has to select the variant track as input, and the sequence track is supplied as a parameter. This means it is more obvious that it should be selected, and it also means that the choice of sequence track will be remembered for the next vcf export.
  •  The folder viewhas been improved with the following:
    • It is now possible to drag and drop objects from the folder editor. This will create a copy of the objects at the selected destination.
    • Attribute columns will be left empty if the attribute has not been defined (previously attribute values that had not been defined were set to 0 and checkboxes were shown as unchecked).
    • A new column showing the first 50 residues of each sequence has been added as an option.
    • The column with the name “Length” has been renamed to “Size”.
    • The column “Size” shows the length of a sequence, or for sequence lists, the number of sequences e.g.:
      • Sequence or contig lists: the number of sequences/contigs
      • Read mappings: the length of the consensus sequence
      • De novo assemblies: the length of the reference
      • Alignments: the length of the alignment
  • The Side Panel “Save/Restore Settings” functionhas been expanded with a new feature:
    • The “Save/Restore Settings” function (found at the top of the Side Panel) has been redesigned. It is now possible to save settings in two different ways. 1) The settings can be saved for this element type in general, e.g. for a track it would be save settings “For Track View in General”. In this way the settings will be applied each time you open an element of the same type, which in this case means each time one of the saved tracks are opened from the Navigation Area, these settings will be applied. These “general” settings are user specific and will not be saved with or exported with the element. 2) Settings can be saved with the specific element only e.g. for a track it would be save settings “On This Track Only”. The settings are saved with only this element (and will be exported with the element if you later select to export the element to another destination).
  • Alignments: If you have one particular sequence that you would like to use as a reference sequence, it can be useful to move this to the top. This can now be done automatically by right clicking on the sequence name and then selecting “Move Sequence to Top”.
  • The Sequence List Table has been improved with a new feature. A new column showing the first 50 residues of each sequence has been added as an option.
  • SOLiD import now accepts XSQ files
  • The following Plug-ins are now fully integrated in the Workbench:
  • The tomato genome, Solanum lycopersicum SL2.40.18, available in the Download Genome tool.
  • Phylogenetic trees:
    • Create Tree now support the Kimura 2-parameter substitution model for DNA sequences and Kimura's distance estimate for protein sequences (Kimura 1983).
    • It is now possible to construct Maximum Likelihood phylogenies from protein sequences.

Improvements

  • Scrolling in read mappings: The mouse scroll speed through read mappings can now be performed with increased speed. Shift + Alt + Mouse wheel scroll makes the scroll 10x as fast as when using Alt + Mouse wheel scroll. When zoomed all the way in, each mouse wheel step scrolls 10 rows.
  • Sort Sequences by Name: The multiplexing tool now allows a delimiter between group names in the “Sort Sequences by Name” wizard. This means that the selected group names are separated by an underscore. Previously all selected group names were merged without any delimiter.
  • Cloning: The cloning editor can now work without having a designated vector. In essence this means that when no vector is selected you go directly in “Stitch mode” when a fragment has been selected, whereas you go in “Cloning mode” when a cloning vector and a fragment are selected.
  • Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
  • Filter Annotations on Name: The wizard layouts for the tool when used directly as opposed to when included in a workflow has been standardized.
  • Extract consensus sequence tool:
    • It is now possible to use the quality scores when resolving conflicts or disagreements between reads with “Insert ambiguity codes”. Previously, “Use quality scores” could only be selected when using the “Vote” option for conflict resolution.
    • Low coverage regions are now annotated in the consensus sequence produced.
    • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking a selection on the reference sequence in the mapping view, enabling the user to extract part of the consensus sequence.
    • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking the name of the consensus or reference sequence, or when clicking the Extract Consensus button in the mapping table. The right-click menu option on the consensus to Open Sequence Including Gaps has been removed, since this functionality is now covered by the Extract Consensus Sequence tool.
  • When using the “Translate to protein” tool, the max limit has been raised to 1GB.
  • The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence".
  • The alignment tool is now more memory efficient.
  • Tables: Improved auto-adjustment of the column width (based on content and number of columns).
  • Read mapping: The speed of running a read mapping against a masked reference has been improved significantly. When mapping reads to a reference sequence, it is possible to map reads to only selected annotated regions of the reference (= masking). Previously masking of a reference was performed by replacing the masked out nucleotides with N's. The new masking method discards the masked out nucleotides by splitting the reference into separate sequences. Hence, the masked out sequences are completely ignored in the analysis. The remaining sequence fragments are positioned according to the original unmasked reference sequence.
  • Read mapping: The status bar in the lower right corner now shows the corresponding positions on the reference/contig sequence.
  • The read mapper will now place ambiguous gaps to the left, as opposed to the right, to ensure better concordance with common variant databases.
  • BLAST has been upgraded to BLAST+ 2.2.28 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.28 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777.
  • Usability improvement of simple table filtering:
    • A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
    • For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.
  • Phylogenetic trees:
    • Bootstrapping with the "Maximum Likelihood Phylogeny" is now possible.
    • Bootstrap values are now displayed in percent instead of absolute numbers.

Bug fixes

  • Numbering of amino acids when calculating amino acid changes was wrong for coding regions spanning the starting point of circular chromosomes. We recommend running amino acid calculation again. Please note that the actual amino acid change is called correctly, only the numbering is affected.
  • PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.
  • Phylogenetic trees:
    • The Juke-Cantor distance estimate now ignore all positions containing gaps in pairwise alignments.
    • Disabled substitution rate estimation when the corresponding option is deselected by the user in the Maximum Likelihood Phylogeny tool.
    • Fixed a bug that caused branch lengths to be estimated incorrectly for ML trees.

Changes

  • Option to calculate RPKM values for genes without associated transcripts has been added to RNA-seq analysis.
  • System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0.
  • Secondary Peak Calling: The parameter “Fraction of max peak height for calling”, in the “Secondary Peak Calling” wizard,  has been changed to use the interval 0-1with 0.2 as default setting. Previously the interval was 0 – 100 with 20 as default setting.


QIAGEN CLC Genomics Workbench 5.5.2

Release date: 2012-12-07

Bug fixes

  • Fixed a number of mapper errors causing the mapper to crash.
  • Fixed a problem in the read mapper when estimating paired distances. This lead to very few reads mapping as pairs.
  • Fix to the proxy settings recognition meaning that Download Genomes and download of BLAST databases now work when there is a proxy setup.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Fixed a problem sorting sequence lists on modification date.
  • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
  • Various bug fixes.


QIAGEN CLC Genomics Workbench 5.5.1

Release date: 2012-09-05

Improvements

  • Improved accuracy of read mapping

Bug fixes

  • Important: In Genomics Workbench 5.5, the Process Tagged Sequences tool would sometimes switch the sample names of the results. We strongly recommend everybody to update to the new version, and re-run all analyses made with this tool in Genomics Workbench 5.5.
  • Fixed: Various read mapper bug-fixes that made the read mapper crash on certain data sets
  • Fixed: Workflows would fail when intermediate results were empty (e.g. if no variants were found and a variant track was used for subsequent analysis).
  • Fixed: Consensus generation when creating standard read mappings was slow in Genomics Workbench 5.5
  • Fixed: Some IonTorrent sff files would fail to import on Windows.
  • Various bug fixes


QIAGEN CLC Genomics Workbench 5.5

Release date: 2010-08-10

New features

Resequencing tools

  • New variant caller: Probabilistic variant detection.
    • This is based on a probabilistic model in contrast to the quality-based variant caller that is based on quality analysis and cut-offs.
    • Supports genomes with a ploidy of 1, 2, 3 or 4.
    • Pre-filtering for non-specific matches and intact pairs
    • Post-filtering of homopolymer regions and forward/reverse reads balance
  • The current SNP and DIP detection tools are merged into one: Quality-based Variant Detection
    • Pre-filtering for non-specific matches and intact pairs
    • Post-filtering of homopolymer regions and forward/reverse reads balance
  • Target regions statistics(previously a plug-in) is now integrated into the Workbench
    • A new parameter: Minimum coverage that will report the fraction of each region that is covered by at least this number of reads
    • Works on tracks: the regions of interest are defined in a track and the resulting per-region table is reported as a track
  • Annotation and filtering tools for variants
    • Annotate and filter against database variants (dbSNP, 1000 genomes or other databases that can be downloaded or imported)
    • Filtering of marginal variant calls based on average base quality, forward/reverse reads balance and frequency
    • Annotating variants with exon numbers
  • Variant comparison
    • Compare variants within group: Find variants that are shared between a number of samples
    • Fisher exact test: Compare variants between case and control groups to find variants that are more common in the case than in the control
    • Trio analysis: Compare child-father-mother variants to enable studies of inherited and de novo mutations
    • Filter against control reads: Compare a variant track against a control sample to remove variants that are also present in the control
    • Filter on haplotype comparison: Identifies variants that have the same haplotype in two samples.
  • Functional consequences of variants
    • GO enrichment analysis.This tool can be used to investigate the effect of candidate variants by analyzing the affected genes for a common functional role.
    • Amino acid changes: Classify synonymous and non-synonymous variants and see the effect on the protein.
    • Annotate with conservation scores: Annotate a variant with a score from conservation tracks that can be imported into the Workbench.
    • Predict splice site effect: A simple investigation to see if the variant is within two bases of an intron-exon boundary

Download of reference genome and annotations

  • Integrated download of reference genome sequences and annotations for selected organisms
  • Example: for human hg19, you can directly download sequences, genes and transcripts, variants from 1000 genomes, Hapmap, COSMIC, and dbSNP (incl. common SNPs).

Tracks

  • Genomic information for re-sequencing analysis can now be stored as tracks.
  • Great power for comparison and visualization because different kinds of data (reads, variants, genes etc) are not bundled into one static file but are separated into one file per data type. This means that different data sources can be compared and visualized in a flexible way.
  • Track lists provide a mechanisms for combining several de-coupled tracks into one list for visualization purposes while retaining the individual files that contain the data
  • All tools for re-sequencing has options to create and use tracks (e.g. read mapping, variant detection etc). More tools will be re-designed to work with tracks later.
  • Tools for converting between standard sequences and mappings and tracks:
    • Convert tracks to sequences, mappings etc
    • Convert sequences, mappings and annotations to tracks
  • Tools for filtering, annotating and merging tracks
  • Support for importing files as tracksfrom a number of new formats:
    • Fasta
    • VCF
    • BED
    • Wiggle
    • UCSC table format
    • GFF / GTF and GVF
    • Complete genomics master var files

Workflow

  • Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
  • Workflows can be distributed and installed either in the Workbench or in the QIAGEN CLC Genomics Server
  • The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
  • The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
  • Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

New read mapper

  • Great improvement of speed for mapping (white paper to be released soon)
  • Support for complex genomes with many repeats
  • Re-design of wizard for read mapping to make it simpler and easier to use. Options to control consensus sequence building and annotating with conflict annotations have been removed, since they have very little relevance for the amounts of data created by NGS platforms today
  • Color space mapping is still performed with the old mapper
  • Automatic calculation of paired distance (only for base space data)
  • Report includes percentage of reads instead of only counts
  • Changed strategy for placement of gaps: previous versions tried to cluster gaps into as few units as possible. This would sometimes cause problems for variant calling because this would in some situations place the gaps differently from read to read.
  • Please note that the memory requirements are different than for the old mapper. The memory requirements depend largely on the size of the reference genome. We will soon update our system requirements page to reflect this.

Sequencing QC report: Create summary statistics for sequencing data in various ways:

  • General statistics on read length etc
  • Quality statistics on quality scores
  • Over-representation analysis of subsequences
  • Analysis of duplicated reads

Re-organization of menus in general to be more genomics focused

  • Classical sequencing tools organized into a subfolder (for gene and protein analysis, alignments and trees etc)
  • Molecular biology tools like cloning, PCR primer design, Sanger sequencing analysis etc moved to a special folder
  • Two new folders for core NGS and core track tools
  • Application-specific folders for the various types of NGS applications: resequencing, de novo sequencing, transcriptomics and epigenomics
  • Search tools moved to the Download menu (available from the top menu and the Tool bar)
  • Different importers integrated into one menu, including the new track import. The Vector NTI import has been moved into a plug-in that can easily be installed from the plug-in manager.
  • The Local Search has been moved from the Search menu (now renamed to Download) and into the Edit menu

Special notes for customers already using the Genomics Gateway plug-in

  • New search tool in track list editor
  • New navigation and position panel at the top of the Side Panel in the track editor
  • Download tool for downloading genomic data replaces Ensembl download tool
  • Unlimited number of chromosomes in tracks
  • More streamlined conversion tools:
  • Convert tracks to sequences, mappings etc
  • Convert sequences, mappings and annotations to tracks
  • Export tracks to gff, sam
  • Print and graphics export of tracks
  • New tool for filtering marginal variant calls
  • New tool for annotating against database variants

Plugin updates

    • Genomics Gateway plug-in is integrated into the standard Genomics Workbench and Server.
    • Probabilistic variant detection Plug-in is integrated into the standard Genomics Workbench and Server.
    • Sequencing QC plug-in is integrated into the standard Genomics Workbench and Server.
    • Target regions statistics plug-in is integrated into the standard Genomics Workbench and Server
  • Grid integration plug-in is integrated into the general server plug-in. If a grid preset is present on the server, the Grid option becomes available in the Workbench dialog.
  • Old read mapper made available as a legacy plug-in that customers can download. This facilitates compatibility of results with previous versions and can be used when memory requirements for the new mapper are too large.
  • Beta read mapper is integrated into the standard Genomics Workbench and Server.
  • Biobase genome Trax is redesigned and split into two:
    • For downloading data (requires a download license)
    • For annotating a variant track (requires an online license)


QIAGEN CLC Genomics Workbench 5.1.5

Release date: 2012-04-11

Improvements

    • Ion Torrent paired protocols are now supported for both fastq and sff files. Read more...
    • MiSeq multiplexed data directly supported. This means that the barcoded samples are recognized on import and the reads are grouped accordingly. The reads from the same sample will be grouped in its own sequence list.
  • New broken pair mate locater tool for getting overview of where the mates of broken pairs in a selected region are mapped. It includes the possibility to extract a sequence list with the broken pairs.
  • Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.
  • User manual includes a section on which tools will be benefit from computers with multiple cores.
  • The license order ID is visible in the License Manager, both for static and network licenses. For security reasons, the last 10 characters of the ID are masked. This will prevent unauthorized persons from copying the license order ID to another computer, but will allow the CLC staff to identify the license used.

Bug fixes

  • Fixed: ChIP-Seq Analysis would sometimes yield no results when the FDR could not be estimated. This error was introduced with Genomics Workbench 5.0.1. If you have had ChIP-Seq samples were no peaks were reported, we recommend re-running the analysis with the new version.
  • Fixed: Cloning bug: when performing restriction cloning in regions with single-stranded DNA, you would get an error.
  • Fixed: 454 paired data import: quality scores on the second part of the read were not imported.


QIAGEN CLC Genomics Workbench 5.0.1

Release date: 2012-02-23

Plug-in updates

Probabilistic Variant Detection Plug-in updated

  • There is a new filter that requires sequencing reads from both strands to call a variant
  • The forward and reverse coverage for each allele is reported in the output

Bug fixes

  • Fixed: Downloading of protein sequences from NCBI fails.
  • Fixed: Calculation of cDNA-level changes in variant detection fails in some situations.
  • Fixed: Trimming tool in Sequencing Data Analysis (not for High-throughput Sequencing data) does not add annotation to sequences when the full sequence should be discarded.
  • Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.


QIAGEN CLC Genomics Workbench 5.0

Release date: 2012-02-13

 New features

  • New de novo assembler.
    • Scaffolding is integrated into the assembly. This means better resolution of contigs and insertion of Ns when two contigs cannot be joined in sequence but there is pair information that connects them.
    • New extended report for the assembly with information about nucleotide distribution, contig lengths measurements and scaffolding regions.
    • User interface improvements: Wizard re-designed to better reflect the process of the assembly. The parameters related to the mapping step are only available when the user chooses to map the reads back to the contigs.
    • New parameter for specifying the maximum bubble size. There is a default value which is automatically calculated based on the input data.
    • New white paper with benchmarks and results from quality control.
    • The old de novo assembler is available as a plug-in. At the end of 2012, the plug-in will be discontinued, so it should only be used for backwards compatibility with results from older runs or if the new assembler fails.
  • Printing and pdf export of read mappings: the mappings are now wrapped to make better use of the paper.
  • SNP and DIP detection results include cDNA-level numbering and variant information compatible with www.hgvs.org/
  • SAM files exported from the Workbench now include basic information about read groups. Furthermore, read orientation for paired reads is now preserved when exporting to SAM and BAM files.
  • Improved exploitation of multi-core machines in read-mapping, RNA-Seq, and de-novo assembly.
  • Improved performance and memory management for high-throughput analyses in general.
  • Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
  • "Show" submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
  • The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
  • The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.
  • VectorNTI import is no longer in a separate plug-in but part of the Workbench. The functionality remains unchanged.

Plugin updates

  • Genomics Gateway plug-in updated
    • New tools for analyzing variants in groups of samples, enabling systematic analysis of genetic variants for whole genome, exome or targeted approaches.
      • Find Common Variations in Group. This can be used to find common variants in a group of variant tracks.
      • Fisher Exact Test. Comparing two groups of variant tracks (e.g. can be used for case-control studies). You can see which variants are found more common in the case compared to the control group using the Fisher Exact test.
      • Filter against Control Reads. This can be used to compare a single case variant track against a negative control from the same sample. It will check whether a certain number of the reads in the control sample have the same allele present as in the case variant.
    • New tools for functional annotation of variants
      • GO Enrichment Analysis for identifying significant gene ontology terms, which are annotated to genes having at least one variation.
      • Annotation with Conservation Scores. By importing a conservation score track (e.g. PhyloP Scores), variants can be annotated with a conservation score. Variants with a high score are assumed to alter functionally important regions.
    • New data structure.
      • All tracks are now saved as single files, and you can create a Track List to visualize them together.
      • A tool is available for data conversion from track sets to single tracks
    • New organization of the "Tool box" to provide a better overview
    • Support for batching and running tools on a Genomics Server
    • The Track List view supports drag and drop for adding and re-arranging tracks
    • Several Graph tracks can be created and displayed
  • Probabilistic Variant Detection Plug-in updated
    • The probability used as threshold for the algorithm is now reported in the output
    • Variants reported cDNA-level numbering and variant information compatible with www.hgvs.org/
  • Additional Alignments Plug-in updated
    • The algorithms have been updated to the most recent versions
    • The list of algorithms has been reduced to two for compatibility reasons


QIAGEN CLC Genomics Workbench 4.9

Release date: 2011-11-29

New plug-ins and plug-in updates

  • New plug-in released: Ab Initio Transcript Discovery Brand new tool for transcript discovery. Based on gapped alignments of RNA-Seq data, the plug-in identifies new transcripts and creates or extends annotations on the reference sequence that can be used for measuring gene expression using the RNA-Seq Analysis tool of the Genomics Workbench. The plug-in provides functionality a la Cufflinks/TopHat. Note that this used to be called the Large Gap Mapper plug-in.
  • Genomics Gateway plug-in updated
    • New refiner: variant frequency. This allows you to filter a variation track, so that only the variants that have a frequency above a user-defined threshold remain. Note that the filter only applies to the frequency of non-reference alleles.
    • Performance improvements when visualizing read tracks
    • Fixed: CDS annotations from Ensembl did not include start codons
    • Fixed: Some variation tracks were not always recognized as variations. This means that the variation-specific refiners could not be used.
    • Fixed: Table view of annotation tracks could have a very large number of columns that are now combined into one column.
    • Fixed: There was an error when closing a view without saving changes. This could lead to subsequent errors when trying to rename tracks.
  • MLST module updated
    • Possible to download MLST schemes from any web site compatible with mlstDBnet
    • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than “New allele”
  • Structural variation plug-in updated
    • Only detection of insertions, deletions and interchromosomal variations are now supported.
    • The plug-in has a problem with repeats. The best way to work around this is to ignore non-specific matches when doing the mapping, to run the structural variant detection with a very stringent p-value cutoff and filter repeats out afterwards if possible (this could be by refinement with the microsatallite track from Biobase or another repeat track using the Genomics Gateway).
    • Integration of exporter to export results in circos format.
See a list of all plug-ins here.

New and improved features

  • Process tagged sequences
    • A summary report is now available with an overview of the number of reads per bar code.
    • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
  • Core management:  you can restrict the maximum number of cores that the Workbench is allowed to use. This can be useful when the Workbench is running on a system with shared resources where other applications need reliable access to CPU when the Workbench is doing analyses. This is mainly an issue for the De novo assembly and Read Mapping algorithms but the restriction applies to all algorithms that use several cores.
  • Multi-site Gateway Cloning . You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning.
  • Find Binding Sites and Create Fragments improved:
    • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
    • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
  • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
  • Enhancing the nomenclature of reporting amino acid changes in variant detection:
    • p. prefix included
    •  ? used for unknown (rather than non-standard “Unknown”)
    • = used to denote an allele which agrees with the reference sequence (rather than missing entries or entries like Ala45Ala)
    • [...] used around ,-separated lists of changes, each change coming from a different CDS annotation
    • [...];[...] scheme used to separate multiple alleles at same site

Bug fixes

  • Fixed: Import of SOLiD data failed when multiple sets of paired data was selected.
  • Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.
  • Fixed: Set-up experiment would crash when using many samples.
  • Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.
  • Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed.
  • Fixed: Motif search did not exclude regions with Ns when the option “Exclude matches in N-regions for simple motifs” was selected.


QIAGEN CLC Genomics Workbench 4.8

Release date: 2011-10-12

New plug-ins and plug-in updates

New and improved features

  • De novo assembly improvements:
    • Word size can now be manually adjusted
    • When update contigs is not selected, the resulting mapping table will also include contigs where no reads map back. This means that the number of rows in the table will be identical to the number of “Simple contigs” produced by the de novo assembler. Previously contigs with less than two reads mapped back would be omitted from the table.
  • Merge Mapping Results will produce a mapping table when mapping tables are provided as input
  • New button to extract a subset of mappings from a mapping table
  • Mapping tables now include a row for reference sequences where no reads map. This is done to provide consistency of results. Opening such an entry in the table will just open the reference sequence in the table.
  • You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad.
  • SNP detection no longer ignores ambiguity bases in the reads. Each ambiguity code is treated as a separate variant; no merging of the possible variants covered by each ambiguity code is attempted (this typically only has an effect when using Sanger sequencing data since standard NGS platforms do not use ambiguity base calls).
  • Translation in the Side Panel of nucleotide sequences now includes options to translate “All forward” or “All reverse” reading frames.
  • Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position.
  • Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment.
  • Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list.
  • Restriction enzymes updated with latest REBASE version.
  • Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu.
  • SAM import and export format is now described in detail in the user manual.

Bug fixes

  • Fixed: Orientation of SOLiD mate-pair data was not set correctly on import. This meant that the reads were marked as broken pairs after mapping. We strongly recommend all users to re-run the import if using SOLiD mate pair data.
  • Fixed: Virtual tag lists created with RNA failed
  • Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules.
  • Fixed: Experiments tables can now be exported in Excel and csv formats
  • Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of QIAGEN CLC Genomics Workbench 4.7
  • Fixed: If a combination of trim options is used, like quality trim or length trim in addition to adapter trimming on both strands, the reads could end up reverse complemented.
  • Fixed: Import of paired data generated by Illumina Casava 1.8 did not match the pairs correctly. Users are advised to re-import and re-analyze all data imported from Casava 1.8.
  • Fixed: Pattern discovery wizard failed when the tool is run for the second time.
  • Fixed: De novo assembly sometimes failed on Mac OS 10.7 Lion.
  • Fixed: Errors for read mappings with the text “premature end of .cas file” have now been fixed. This has only been a problem on Windows.
  • Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format.


QIAGEN CLC Genomics Workbench 4.7.2

Release date: 2011-07-14

Bug fixes

  • Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
  • Fixed: The UniProt search has been updated to reflect URL-changes at uniprot.org.
  • Fixed: A problem with interpretation of broken pairs on re-import from SAM format files.
  • Fixed: A problem with microarray experiments where large experiments could not be analyzed.


QIAGEN CLC Genomics Workbench 4.7.1

Release date: 2011-06-27

Bug fixes

  • De novo assembly produced empty results
  • Paired distances for read mapping were not recorded correctly in history
  • Read mapping in batch: the minimum and maximum paired distance fields were enabled even though the “Override” checkbox was unchecked
  • Improved performance of packed view rendering
  • Various minor bug-fixes


QIAGEN CLC Genomics Workbench 4.7

Release date: 2011-06-21

New and improved features

  • Mapping
  • New plugin to detect Structural variation
    • Action to detect structural genomic variation from paired read information
    • Action to detect copy-number variation (CNV) from coverage information
  • New and more flexible data structures to store information about paired data
  • All history entries will from now on include the version number of the software
  • Previous limit at 2 billion for the maximum number of reads in one analysis has been removed.
  • Reporting of amino acid changes in SNP and DIP detection now follows recommended nomenclature more closely w.r.t. changes that affect start codons and changes that cause indels at the amino acid level.
  • Performance of Excel 2010 exporter improved in terms of speed and memory requirements
  • When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server.
  • Export of trace data in scf format.
  • BLAST
    • BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
    • The “Mask lower case” option has been removed
    • Tool to download BLAST databases from NCBI within the Workbench
    • The BLAST Database Manager has been improved to show when referred databases are missing

Bug fixes

  • Fixed: References between SNP tables and mapping results were broken when exporting-importing data.
  • Fixed: Summary mapping report did not mention customized mapping parameters when running in batch mode
  • Fixed: Various SAM/BAM import and export errors
  • Fixed: When running adapter trimming searching on both strands, some reads were marked as “reversed” in the result. The only consequence is incorrect reporting of the number of forward and reverse reads in the mapping results.
  • Fixed: Mapping report did not calculate read length for individual reads when using paired data
  • Fixed: Alignment-based primer design failed for columns with many gaps
  • Fixed: “Find Binding Sites and Create Fragments” did not find binding sites where the primer extended the 5′ end of the template sequence
  • Fixed: DIP detection would crash on large data sets
  • Fixed: Import of certain special Genbank files failed
  • Fixed: RNA-Seq report with paired data: total number of reads was counted as pairs rather than individual reads
  • Changed: RNA-seq transcript variants are named using ‘.’ rather than ‘_’. Note that it is not possible to create transcript-level experiments based on old and new samples
  • Changed: Label of Illumina quality score selector has been changed to reflect the 1.8 update of the Illumina pipeline which now uses quality scores on the Phred scale
  • Various minor bug fixes


QIAGEN CLC Genomics Workbench 4.6.1

Release date: 2011-04-06

Bug fixes

  • RNA-Seq would crash when selecting prokaryote as organism type


QIAGEN CLC Genomics Workbench 4.6

Release date: 2011-04-05

New and improved features

  • Import of Ion Torrent data. A special importer has been made for Ion Torrent data in fastq or sff format. Read more.
  • Checkbox for reporting merged SNPs. Read more.
  • An adapter trim setting for SOLiD 50bp small RNA reads has been added. Read more about adapter trimming.
  • SNP detection: When minimum paired coverage is set, reads from broken pairs will be completely ignored. Read more.
  • DIP detection: Reporting of amino acid changes better reflects nomenclature consensus.
  • RNA-Seq: the transcript-level sample includes a column for the ratio of unique to total transcript reads. Note that this means that results generated with this version cannot be used in older versions. Read more.
  • Better support for color space SAM/BAM files.
  • Local BLAST is faster when blasting against small databases
  • Export in color space fastq format. When data is marked as color space, exporting in fastq format will produce a file with color encoding rather than bases.
  • The plug-in used by the Workbench can now be installed using the Download Plug-ins tab in the Plug-in Manager.

Bug fixes

  • Fixed: In certain situations, the data-specific parameters in read mapping did not take effect
  • Fixed: When running read mapping in batch, the data-specific parameters were only applied to the first data set in the batch
  • Fixed: Local BLAST did not work on Mac OS 10.5
  • Fixed: Read mapping and RNA-Seq crashed because the reference could not be found.
  • Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor.
  • Fixed: Import of csfasta paired data crashed when one read had a dot in the beginning of the sequence.
  • Import of paired qseq files: the read pairs are now joined correctly when importing paired qseq files
  • Fixed: Import of GO annotation files did not work
  • When processing tagged paired data sets, the status of the resulting files were not marked as paired. This means that subsequent analyses did not make use of the paired information.
  • Various minor bug fixes


QIAGEN CLC Genomics Workbench 4.5.1

Release date: 2011-02-18

Bug fixes

  • Fixed issue with synonymous overhang characters in cloning editor
  • Graphics export now works with restriction sites shown
  • Gene Ontology Annotations can now be imported
  • CHiP-seq analysis adjusted for the use of gapped aligner – CHiP-seq analysis with previous version should be redone
  • Improved support for Mac OS X systems with japanese language
  • Improved support for systems with 512 MB of memory or less
  • Blast: Fixed issue with BLAST database creation taking too long under certain circumstances
  • Blast: Fixed issue concerning errors when input sequence names contained illegal characters
  • Blast: Fixed issue with Extract And Open option being erroneously disabled
  • Blast: Option to enter custom Entrez Query limits in Blast at NCBI re-introduced.
  • Blast: Improved speed when using Blast results as input to wizards.


QIAGEN CLC Genomics Workbench 4.5

Release date: 2011-01-26

New features:

  • Batching functionality of all high-throughput sequencing tools. It is now possible to start batch runs, e.g. running 12 samples through RNA-Seq Analysis in one go. Read more.
  • RNA-seq: transcript-level expression values and support for paired data
    • Included option to use paired information in RNA-seq. Read more.
    • Expression values can now be stratified into transcript level expression values, both for single and paired reads. Read more.
    • SOLiD data: new algorithm for mapping reads allows much higher fraction of reads to be mapped. Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more.
    • Similarity fraction for mapping of long reads is now available as a user-specified option (this was previously automatically set). Read more.
    • Simple reporting of putative gene fusions when using paired data. Read more.
    • Note about compatibility: Results from earlier versions should not be compared with results from this version.
  • BLAST tools have been redesigned
    • New Blast Database manager for easy administration and management of local BLAST databases. Read more.
    • More user-friendly way of creating and accessing local BLAST databases. Read more.
    • Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets.
    • The SNP Annotation using BLAST tool has been discontinued.
    • See migration notes for using your old databases here.
  • SOLiD data: new algorithm for mapping reads allows much higher fraction of the reads to be mapped.
    • Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more..
    • Note about compatibility: Results from earlier versions should not be compared with results from this version.
  • Multiplexing: Process tagged sequencing data
    • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples. Read more.
    • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses.
  • High-throughput Sequencing Import includes an option to place data into sub-folders (useful for batching subsequent analyses)
  • Cloning tool re-designed to make it easier and faster to perform restriction cloning Read more
    • Restriction sites used to select target vector and fragment. Read more.
    • Sequences can now be displayed in circular mode in the cloning editor. Read more.
    • Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences). Read more.
    • Option to clone several fragments and adjust overhangs and orientation in one dialog. Read more.
    • New cloning tutorial available for a quick introduction. Read more.
  • Improved layout of restriction site annotations
    • Linear view: There is a new option for displaying labels as “Stacked” which means that the labels of overlapping cut sites can be discriminated. Read more.
    • Circular view: There is a “Radial” option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout. Read more.
  • Improved layout of general annotations
    • Linear view: There is an option to separate restriction sites and annotations in separate layers.
    • Circular view: There is a “Radial” option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout.
  • Motif search available in Side Panel
    • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites). Read more.
    • Use motif lists to add your own motifs to the Side Panel.
  • Annotation table now available for sequence lists, mappings, mapping tables, BLAST results and alignments. Read more.
  • SNP detection reports adjacent SNPs within the same codon as one SNP. Read more.
  • De novo assembly: post-processing options when mapping reads back to contig sequences have been expanded. It is now possible to preserve the original contig sequences from the assembler (they used to be replaced by the consensus sequence from the mapping). Read more.
  • Support for exporting tables as tab-delimited files.
  • Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog). Read more.
  • The default database of restriction enzymes can be expanded (requires manual edit of database file). Read more.
  • The default set of codon frequencies can be expanded (requires manual edit of table files). Read more.
  • Improved option to export and import Side Panel settings. Read more.
  • Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB.

Bug fixes

  • SNP detection bug with corrupt complementary CDS annotations.
  • SNP detection: color correction errors now count when filtering SNPs (this has become important with the new mapping algorithm for SOLiD data).
  • The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules.
  • Various bug-fixes


QIAGEN CLC Genomics Workbench 4.0.3

Release date: 2010-10-28

Improvements:

  • Enhanced usability of GSEA analysis wizard: The “Remove duplicates” option is now a check box to switch on and off. Before, the choice of switching off was implicit by choosing Feature ID as the identifier. Now this is explicit using a check box.
  • Improved performance rendering large tables, particularly those with html formatting.

Bug fixes

  • SNP and DIP detection previously ignored overlapping pairs. Now they count (as one read) if they fulfill the quality criteria (SNP detection). In cases where the two parts of the pair disagree, the pair does not count. We recommend running all SNP and DIP detections based on overlapping pairs data sets again (this would be the case if the minimum distance when mapping the reads is lower than two times the read length). There is no need to re-run mappings – just the SNP/DIP detection.
  • ChIP-Seq: “nearest gene” reported not always right. This was the case for the last peak on each chromosome and also in cases where the order of the gene annotations in the reference file did not correspond to the order of the annotations on the actual sequence. We recommend running all ChIP-Seq Analyses again to get the correct reporting of nearest genes. There is no need to re-run the mappings.
  • SNP Annotation Using BLAST failed with certain query sequences (the result could not be shown)
  • Fixed crash of 454 import on certain Linux and Mac systems
  • SOLiD import accepts read names with -P2 at the end
  • Improved import of SAM/BAM files:
    • Better support for files from SOLiD Bioscope
    • Preliminary support for Complete Genomics files (The actual alignment is not represented completely – insertions that relates to a consensus sequence will be represented as unaligned ends in the imported mappings. This should be taken into account when looking for variations.)
  • In the Sequencing Data Analysis-> Assemble Sequences to Reference, the conflict resolution was disabled when not including a reference sequence in the output.
  • When importing sequences from Genbank files, mRNA annotations now prefer taking name after “locus_tag” rather than “product”.
  • Various minor bug fixes


QIAGEN CLC Genomics Workbench 4.0.2

Release date: 2010-08-19

Bug fixes:

  • Fixed error when importing 454 SFF files
  • Fixed error when importing SOLiD data with quality scores when the reads had “.”
  • Fixed error mapping large data sets on Windows 64-bit systems
  • Fixed error when opening tables generated by the Transfac plug-in and the primer search tool
  • Fixed errors when running analyses on experiments generated from RNA-Seq results
  • Genbank export of annotations on the negative strand were not in the right order
  • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
  • Various minor bug fixes


QIAGEN CLC Genomics Workbench 4.0.1

Release date: 2010-08-10

New features:

  • Improved performance of table filtering. Removed limit on the number of rows that can be filtered.
  • Option to search for read names in mapping results (and also sequence lists and BLAST results).
  • Improved performance of conflict table.
  • Better layout of graphics export and printing of mapping results: reference and consensus sequence repeated to provide an orientation context on all pages.
  • Extracting consensus sequence of mapping tables is now running in the background to provide a better user experience.

Bug-fixes:

  • Problem regarding mapping of base-space data erroneously in color space. Under special circumstances, the user settings file contained the wrong default parameters and caused the mapping to be in color space rather than base space. We recommend running mappings performed in Genomics Workbench 4.0 again with Genomics Workbench 4.0.1.
  • Fixed problem with SNP detection on large data sets suddenly running very slow.
  • Scalability improvements in mapping and de-novo assembly with drastic improvements in performance
  • Fixed various problems regarding editing alignment and read mappings.
  • In the detailed mapping report, the zero coverage section was empty when there was only one reference sequence.
  • Various smaller bug fixes.


QIAGEN CLC Genomics Workbench 4.0

Release date: 2010-06-15

New features:

  • Small RNA Analysis
    • Brand new tool for analyzing small RNA (including miRNA) data sets
    • Adapter trimming
    • Counting of tags
    • Annotation using miRBase and other resources
    • Visualization of miRNA variants
    • Expression analysis
  • Renaming and redefining concepts
    • Reference assembly -> Read mapping. We adjust to the common term used today for aligning sequencing reads to a reference sequence.
    • Contig -> Read mapping. The result of read mapping was previously called a contig (i.e. the alignment of reads to a reference sequence). Now, the term “contig” is used exclusively for results from de novo assembly. The result of mapping reads is called a “read mapping”.
    • Paired-end -> Paired. We now distinguish during import between Paired-end and Mate pair data. Once imported, there is no difference, and they are both called “Paired”.
  • Trim redesign
    • Brand new adapter trimming including library of adapters
    • Performance improved
    • Multiple data sets supported as input
    • Summary report of the trimming
  • Improved SAM/BAM import
    • BAM format now supported, both import and export
    • More robust implementation
    • Better performance
    • Preview panel making it easier to match reference and SAM/BAM file
    • Reference sequence name spaces automatically converted to underscores when comparing with SAM/BAM file
  • High-throughput Sequence Data Import
    • Gzip support
    • SOLiD fastq format supported (when downloading SOLiD data from Sequence Read Archive, SRA). Read more
    • 454 paired data: Support for both FLX and Titanium linkers (also the possibility to add custom non-palindromic linkers). Read more
    • Improved support for SOLiD paired-end data. Read more
    • Support for data from Illumina Pipeline 1.5. Read more
    • Import of tabular alignment files: it is now possible to specify a read name from the file to be imported with the read. Read more
  • Better compression of reference sequences (lower memory footprint and disk space usage)
  • Performance improvement of read mapping algorithm
  • Improved memory management in general: lower memory footprint and shorter management overhead pauses.
  • Improved memory handling of large tabular data sets.
  • RNA-Seq:
    • Directional RNA-Seq. Read more
    • Exon-intron reads are now counted under Total exon reads. When comparing new and old samples, please re-run the analysis on the old samples to ensure consistency. Read more.
  • New de novo assembler has replaced the old one, making the de novo assembly plug-in obsolete. Read more
  • SNP and DIP detection
    • Dialog usability improved by adding an advanced panel for advanced users
    • Minimum counts have been made more clear by creating a Minimum and Sufficient count
  • Contig report has been renamed to Detailed Mapping Report and has been split up to support data with many reference sequences (e.g. when mapping against contigs from de novo assembly). Read more.
  • Redesign of product graphics
  • Improved consistency of data handling including faster listing of folder contents
  • Performance when saving small files significantly improved
  • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • REBASE collection of enzymes updated to latest version
  • BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
  • Process tagged sequences: it is now possible to input barcodes on a comma-separated list. Read more 
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1’000’000 or 1 000 000). Read more
  • It is now possible to pause and restart processes involving read mapping and de novo assembly (except the accelerated mapping part of the analyses). Read more
  • Normalization of expression data: it is now possible to do “Reads per 1,000,000″-style normalization of count-based data. Read more
  • New preference group called “Data” to hold information about adapter sequences and Gateway cloning primer additions. Read more

Bug-fixes:

  • Print of folder content now takes settings in the Side Panel into account
  • Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
  • Better memory handling in conflict table
  • Read mapping: fixed windows errors on large data sets, fixed color space errors
  • RNA-Seq: max number of mismatches when running color space data could be set to three in the dialog but did not take effect. Now the limit at 2 is enforced in the dialog.
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters


QIAGEN CLC Genomics Workbench 3.7.1

Release date: 2010-02-04

Bug fixes:

  • Fixed error concerning naming of dots in PCA plot
  • RNA-seq: reads that extend over more than two exons are now shown correctly
  • Error in folder editor that prevented all elements to be shown is fixed
  • Documentation on trim using quality scores has been updated
  • Names of results from reference assemblies are now named according to the input data
  • Fixed error preventing manual editing of contigs under special circumstances
  • Various bug fixes


QIAGEN CLC Genomics Workbench 3.7

Release date: 2009-12-15

New features

  • Global alignment for long reads when running reference assembly algorithm
  • Gapped color-space alignment when running reference assembly
  • Significantly improved speed of all operations with large data sets
  • RNA-Seq analysis:
    • Performance optimization: A run of 44 mio reads against the mouse genome now takes 32 minutes on an eight-core computer with 32GB RAM. This used to be more than two hours. With the previous version, a lot of small temporary files were created and deleted, and this took a long time and impacted the comupter’s general responsiveness. In comparison, only a small fraction of temporary files are created with the new version.
    • New option to specify minimum required exon-overlap of reads spanning an exon-exon junction. Read more…
    • New RNA-Seq report which gives statistical overview of the assembly process. Read more…
    • Result table now reports number of exon-exon- and intron-exon junction spanning reads.
    • Result table now reports chromosome location of genes. Read more…
    • Visualization of reads that span exon-exon junctions. Read more…
    • Reads mapping equally well to intron-exon and exon-exon boundaries are now identified as unique exon-exon spanning reads.
    • RPKM is better defined in the user manual. Read more…
    • Default setting for multi-hits is now 10 as in the Mortazavi paper Read more…
    • Very short reads are now assembled allowing more mismatches.
  • Expression analysis:
    • Volcano plots: you can now choose the values to plot on the x-axis. Choose between “Difference” and “Fold change”. Read more…
    • Table view of bar plots shows the same intervals as are shown in the bar plot.
    • Generic importer for expression array data in tabular format. Read more…
    • Generic importer for expression experiment annotation data in tabular format. Read more…
    • Gene Ontology (GO) files can now be used to annotate an expression experiment. Read more…
    • Tag profiling: You are no longer allowed to annotate tag samples, only experiments
    • Side panel of experiment table has been re-organized to provide better overview. Read more…
  • Import high-throughput sequencing data
    • Import tool moved from Toolbox to File menu and tool bar. Read more..
    • Import and export of the SAM alignment format. Read more…
    • Import of alignment data in tab-delimited format, including the ELAND alignment format. Read more…
    • Import of Illumina QSEQ file format. Read more…
    • Linker in 454 data is also found for non-perfect matches Read more…
  • Enhanced visualization of contigs:
    • Un-aligned nucleotides on the inside of paired-end reads are now shown
    • Paired-end reads have a single line connecting the pair rather than gaps
    • Drag handles to move the aligned/unaligned border are only shown when you can see the bases of the reads. This means that you need to have zoomed in to 100% or more and chosen Compactness levels “Not compact” or “Low”. Otherwise the handles for dragging are not available (this is done in order to make the visual overview more simple). Read more….
    • It is possible to display pairs that overlap
  • The unassembled reads from an assembly now preserves their paired-end status (this also means that you can get two lists – one with pairs and one with the remainder of the broken pairs
  • SNP detection output table now reports if multiple non-synonymous SNPs exist in same codon
  • SNP detection dialog: Quality filtering is no longer disabled when quality scores are missing. Due to performance issues it is not possible to check if quality scores are present. The SNP detection will just omit the quality score filtering if quality scores are not present.
  • SNP detection: possible to detect variants with frequency less than 1 percent.
  • Contig report now includes information about coverage for both covered regions and whole reference. Read more…
  • Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
  • The trim functionality now includes the option to trim away a predefined number of nucleotides from either end of a read. Read more…
  • Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones. Read more…
  • Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments. Read more…
  • In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu. Read more…
  • Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments. Read more…
  • Deployment
    • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more…
    • Support for removing tools accessing the internet (NCBI BLAST, update notifications etc). Read more…
  • General import and export
    • Support for import of complex regions from GFF files
    • Export tables and reports in Excel format.
    • Import section of user manual re-structured to provide better overview Read more…. Expression data importers are now described in technical details in a separate section Read more….
    • You can now export multiple sequence lists in fasta format
    • Forced import of zip files is now supported (it will force import the contents of the zip file)
    • The standard import now accepts gzip and tar files as well as zip
    • If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
    • Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
    • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
    • When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
    • GFF plug-in has been updated to accept complex annotations
  • Miscellaneous
    • Advanced retyping of annotations using the annotation table. Read more…
    • Improved reporting of situations when a full disk prevents saving of data
    • Downloading sequences using drag and drop from the search table no longer creates a “Downloading…” node in the folder. The download process can be monitored in the Processes tab.
    • Primer design now supports PCR fragments longer than 5000 bp.
    • Extract Sequences moved from File manu to Toolbox-> General Sequence Analysis. Read more…
    • Better progress feedback on various dialogs

Bug-fixes

  • Problem with order of genes when setting up RNA-Seq experiments. If the order of input sequences was not the same for all samples, the experiment would be wrong.
  • Fixed wrong orientation of SOLiD mate-pair data
  • Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).
  • Fixed problem displaying the “Copying…” label when copying data and then updating the folder
  • Misleading label when assembling reads shorter than 15 bp. Now it says that these reads will be ignored in assembly


QIAGEN CLC Genomics Workbench 3.6.5

Release date: 2009-08-18

New features

  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
  • Export of sequence data in fastq format
  • Now possible to perform detailed manual editing of contigs with up to 100,000 reads
  • Improved performance when zooming large contigs displaying a coverage graph
  • Now possible to change the linker used when importing 454 paired-end data

Bug-fixes

  • Fixed problems importing expression annotation files
  • Fixed error when trimming for vector sequences
  • Fixed tblastn numbering issue
  • Various bug-fixes
This update is recommended for all users.


QIAGEN CLC Genomics Workbench 3.6.1

Release date: 2009-07-09

Issues resolved

  • Problem when adding annotations to an Illumina array file
  • Error handling annotated tag-data
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Problem when importing color space data alongside a .cas file


QIAGEN CLC Genomics Workbench 3.6

Release date: 2009-06-02

New features

  • Tag profiling: tag-based transcriptomics. Read more…
  • ChIP-Seq analysis is now able to (optionally) use a control sample. Read more…
  • Advanced view of elements in a folder including batch editing. Read more…
  • Create new contig from selection. Read more…
  • Import high-throughput sequencing data: you can now import without quality scores. Read more…
  • Reference assembly of short reads: user can now choose between local and global alignment Read more…
  • Reference and de novo assembly output options have been changed so that you no longer need to decide whether you want a contig table or single contigs. Whenever more than one contig is produced, the Workbench automatically creates a contig table Read more…
  • Contig report for reference assemblies: GC content of the reference sequence now included
  • Extract sequences improvements Read more…
    • Now contig tables, overview BLAST tables and RNA-Seq samples can be used
    • User feedback in the dialog is improved
    • Problem with extracting paired-end reads correctly is fixed
  • mRNA Sequencing tool changed name to RNA-Seq Analysis to reflect the consensus about this naming in the NGS community
  • Heat maps and clustering improved:
    • You can now perform different clusterings on an experiment and save them all. In the Side Panel you can switch between the different clusterings to show the corresponding heat map. Read more…
    • Terminology change in the clustering dialogs: “similarity measure” and “cluster distance metric” are replaced by “distance measure” and “cluster linkage”, respectively.
  • Annotating samples or experiments for expression analysis:
    • This is now possible even if the number of features doesn’t match the number of annotations
    • You can now decide which column in the annotation file to use for matching to the sample or experiment. Read more…
    • Because of this extra option, you can no longer include an annotation file when setting up an experiment. You need to add the annotations afterwards
  • Microarray import improved:Added support for import of more versions of native Illumina BeadChip and GEO expression files
  • “Find” in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)

Bug fixes

  • Assembly against many reference sequences could run out of memory. This is been significantly improved.
  • Integration with the Genomics Server: fixed an error when selecting contigs from a contig table for analysis. This is no longer possible (i.e. you have to save the contig first).
  • Microarray import: Fixed a bug that prevented import of expression data with white spaces in column names.
  • Various bug fixes


QIAGEN CLC Genomics Workbench 3.5.1

Release date: 2009-06-11

Issues resolved

  • Rare failure when importing very large Illumina files
  • Memory problem when mapping against many(>20.000) references
  • Rare concurrency issue when translating DNA->protein in e.g. SNP detection
  • Problem rendering scatter plots without lines
  • Graphics export of contigs
  • ChIP-seq table did not show the right distance to nearest gene


QIAGEN CLC Genomics Workbench 3.5

Release date: 2009-06-02

Data formats

  • Data generated with version 3.5 cannot be read in earlier versions

New features

Bug fixes

  • Fixed error when trimming reads for vectors
  • Fixed out-of-memory error in mRNA sequencing
  • Fixed error in mRNA sequencing when gene annotations were present outside the reference sequence
  • Fixed error when parsing files from Clone Manager (cm5-files)
  • UniProt search works again

Note

  • This version introduces a new data format which is not readable by older versions of the software.


QIAGEN CLC Genomics Workbench 3.2.0

Release date: 2009-03-12

New features

  • DIP detection – automatic examination and reporting of insertions/deletions in reference assembly contigs. In the Toolbox under High-Throughput Sequencing. Can be used together with SNP detection to systematically examine positions where the reads differ from the reference sequence. This eliminates the need for manually inspecting gaps and conflicts in the contig. Learn more…
  • 15% less disk space usage of imported NGS data sets.
  • 25% faster assembly of NGS data sets.

 Bug fixes

  • Under certain circumstances, trim failed on Mac OS X
  • mRNA Sequencing: Downstream/upstream options should be disabled when using un-annotated reference sequences
  • Color space information now shown per default for mixed data sets including color space reads
  • De novo assembly report: sometimes number of reverse matches were reported as negative
  • Corrections to the ACE export
  • Better performance of files with many annotations
  • Fixed an error in RNA Structure Evaluation
  • Fixed error and improved performance of Join Sequences tool
  • Fixed error in Find Binding Sites on Sequence: no longer distinguish between lower and upper case
  • Various small fixes


QIAGEN CLC Genomics Workbench 3.1.0

Release date: 2009-02-26

New features

  • Support for reference assembly of SOLiD data in color space (learn more). You need to reimport your data to make use of color space.
  • Viewing of color space data in contig results (learn more).
  • Option of using non-annotated sequences (e.g. EST-library) for RNA-seq (learn more).

Bug fixes

  • Assembly and mRNA sequencing errors (“Empty match not allowed” and “Could not read from temporary file”) fixed
  • Under special circumstances, quality scores were not aligned correctly
  • SNP detection with an RNA sequence as reference failed
  • SNP detection performance for annotated sequences improved
  • Find in the Side Panel did not support spaces when searching for annotations
  • In the cloning editor under special circumstances, an error occurred when replacing a selection with fragment
  • Sequence statistics codon count were not correct when using RNA sequences


QIAGEN CLC Genomics Workbench 3.0.1

Release date: 2009-02-03

Updates

  • Fixed an error when trimming NGS data
  • Fixed an error in the contig view when deleting a sequence that was selected
  • Fixed an error when changing the filter of a sorted table
  • Fixed error when assembling a mix of paired ends and single reads under special circumstances
  • Fixed error in import of cas file based on SOLiD data from the CLC NGS Cell
  • Fixed a rare error when running SNP detection on a contig table
  • Made mRNA Sequencing accept a sequence list as reference
    • Fixed table view of contigs: sometimes an empty entry would appear which did not reflect the reads at the current position


QIAGEN CLC Genomics Workbench 3.0

Release date: 2009-01-27

New features

Transcriptomics

  • Support for both microarray- and sequencing-based (RNA-Seq) expression data
  • Visualization: Interactive heat map, table and scatter plot views
  • Transformation and normalization tools
  • Quality control tools including principal component analysis, MA- and boxplots
  • Experimental design tools for two- or multiple group comparisons
  • T-tests and ANOVA analysis with support for paired/repeated measures
  • Multiple testing corrected p-values (Bonferroni and/or FDR)
  • Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
  • Ability to import NetAffx annotation arrays and adding annotation to experiments
  • Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. ‘GO’stats or specific protein pathways).
  • Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
  • Facility for annotating sequences from GFF or GTF files (as used by Ensembl and the UCSC Genome Browser), useful for annotating reference genomes before assembly
  • Statistics on numbers of matching and unique gene, exon and exon-exon boundary spanning reads
  • Calculation of gene expression measures (RPKM) from mRNA sequence data and generation of gene expression profiles (RNA-Seq analysis)
  • Discovery of novel transcripts/exons through mapping of mRNA reads to whole chromosomes or genomes, comparing matches with known exons
  • Interactive views of assemblies and derived gene expression data

Assembly

  • Long reads assembly significantly faster
  • No upper limit on number of reads in de novo assembly (there is still a limit regarding the size of the genome)
  • New simple output option for de novo assembly: only generate consensus sequence instead of full contigs. At the last step of the de novo assembly wizard, you can now choose between “Full contigs” and “Simple contig sequences”. The latter option will result in a sequence list with all the consensus sequences. This is much faster and less the demanding for the computer. You can always create full contigs later by running a reference assembly with the consensus sequences as references.
  • Quality of trimming for contamination from own sequences improved. It is now possible to trim off smaller primer sequences.
  • SNP detection:
    • Accepts multiple contigs and table of contigs (the table output includes a new column for the name of the contig)
    • For coding regions (annotated with CDS/ORF annotations): changes on the amino acid level as a consequence of a SNP is now reported (both in the table and in the annotations).
    • General performance improvements
  • Right-clicking a graph (e.g. coverage) on a contig lets you export the data points to a csv file.
  • Contig table shows latin and common name of reference sequences. This is beneficial if you perform a reference assembly against references from different species.
  • Multiplexing – Process Tagged Sequences now has an option to filter away groups with few sequences. This is an advantage if you have very ambiguous barcode definitions where sequencing errors would lead to a lot of “false” groups. These groups can now be filtered because of their small size. (The option is called “Minimum number of sequences” and is found in the third step of the wizard.)
  • Coverage info is now included when you export a table of contigs in ace format. (It contains a “Contig Tag” of type comment (a CT clause) containing a textual description of the coverage in the form “Average coverage: 14.65″. )
  • Coverage info is put into the description of consensus sequences extracted from a table of contigs (this means that if you export to fasta, this information will be included).
  • Importing assemblies with more than one contig creates multi contig tables (ace and cas file import)

Improved user experience of processes

  • Non-modal feedback from processes:
    • When there is a message (e.g. from a BLAST search: not hits found)
    • If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
    • Processes running on the CLC Science Server will notify when they are done.
  • Possibility to open results by clicking the button next to the process
  • Possibility to find and select results in the Navigation Area by clicking the button next to the process
  • You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)

Support for interacting with CLC Science Server

  • Read more at http://www.clcbio.com/index.php?id=1260

3D editor re-design

  • The 3D editor now allows you to select individual structure subunits, residues, active sites, disulfide bridges and even atoms, and to customize their appearance

General improvements

  • Limited mode: when using a license server – if there are no more licenses left, you can still access your data. The Workbench will then run in Limited mode where only a few tools are available (corresponds to the tools found in CLC Sequence Viewer). Click “Limited Mode” in the license dialog.
  • Tables:
    • New advanced filter to use numerical data for filtering and to combined several filter criteria. Click the small button next to the normal filter to see the advanced filter.
    • Visual feedback when sorting and filtering tables
    • Improved automatic detection of column width
  • Performance of graphs and plots improved
  • Local BLAST is upgraded to use NCBI BLAST version 2.2.19
  • More elaborate error reports including error logs
  • You can specify which folder the Workbench should use for temporary files
  • Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
  • The “Find” option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.

Plug-ins

  • Extract Annotations plug-in has been improved:
    • Possibility to specify the naming of the sequences (based on annotation name, type etc)
    • Performance improvements to make it possible to extract annotations of large genomes.
  • MLST plug-in: various bug fixes

Bug fixes

  • Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer’s operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
  • Fixed problem when BLASTing with an empty sequence
  • Various performance improvements and bug fixes


QIAGEN CLC Genomics Workbench 2.1.1

Release date: 2008-11-21

Updates

  • Reference assembly: fixed an error which meant that in some cases, reference assembly produces different results depending on the amount of memory available.
  • SNP Detection: Reads were dismissed because of gaps even though the reference sequence also had gaps.
  • The Side Panel’s Find only high-lighted the first hit. This is now fixed.
  • Fixed error when importing 454 fna/qual files
  • Extract sequences: fixed an error when extracting paired-ends sequences from contigs and sequence lists
  • Local BLAST: solved problem applying command-line parameters, now a checkbox determines whether command-line options should take effect
  • BLAST: it was possible to use a BLAST result as input and database
  • Trace data: fixed an error when deleting parts of an unsaved sequence with traces
  • Better performance when zooming a dot plot
  • Better performance when using the Side Panel’s Find in large contigs and sequence lists
  • When right-clicking a CDS annotation and translating into protein, gaps were erroneously introduced into the protein sequence
  • There was an error related to selecting sequences in the Cloning editor
  • Multi-select (using Ctrl / Command key) did not work for sequence lists
  • Various bug fixes


QIAGEN CLC Genomics Workbench 2.1

Release date: 2008-11-11

Updates

  • Support for paired-end Sanger reads
  • Support for paired-end FASTA reads
  • Improved user interface of High-throughput Sequencing Data import dialog
  • Assembly report includes information about assembly parameters
  • Corrected error when opening multiple consensus sequences
  • Fixed problem with import of NGS data in FASTA format
  • Improved error handling for assembly
  • Fixed issue with contig selections while scrolling
  • Corrected error introduced by overlapping mate-pairs


QIAGEN CLC Genomics Workbench 2.0.4

Release date: 2008-10-08

Updates

  • Fixed problems when assembling large or mixed data sets
  • Ensured correct setting of limit for assembly of short reads


QIAGEN CLC Genomics Workbench 2.0.3

Release date: 2008-10-02

Updates

  • Fixed problems with de novo assembly
  • Status properly updated when a conflict is resolved
  • Assembly programs now run on older version of Linux


QIAGEN CLC Genomics Workbench 2.0.2

Release date: 2008-10-02

Updates

  • Fixed problems when scrolling very large sequences
  • Fixed problem when importing very large GenBank files
  • Improved possibilities for navigating contigs
  • Improved stability when importing non-standard data
  • Improved memory handling and stability of assembly algorithms
  • Support for import of Illumina long insert paired-end data


QIAGEN CLC Genomics Workbench 2.0.1

Release date: 2008-09-18

New features

General performance improvements

  • Improved performance when handling large data sets

High-throughput Sequencing Assembly

  • Support for reference assembly against the human genome (i.e. reference sequences of any size)
  • New and much faster algorithm for assembling short reads (less than 55 nucleotides)
  • Significant performance improvements of reference assembly.
  • True support for reference assembly of mixed data sets in one go. Sequencing data from different platforms (and both single and paired ends) can now be assembled together. Previously this could be accomplished by making separate assemblies and joining the contigs afterwards, but now this process is automated. Read more…
  • Reference sequences can be masked based on annotations. This could be used to e.g. mask off repeat regions or only include exons in the assembly. The reference sequences have to be annotated in order to use masking. Read more…
  • Assembly report includes the number of contigs produced
  • Contigs from a reference assembly can also be shown in an overview table. This was previously only possible for De novo assembly. In the last step of the reference assembly wizard, there is an option: Create overview table including all contigs. Read more…

Import and export

  • Support for high number of Sanger sequencing data with trace information. Using the Import functionality under High-throughout sequencing you can import huge amounts of e.g. abi files. This will import quality scores but discard trace data to produce a sequence list in the Workbench which makes it possible to assemble thousands of Sanger reads. Read more
  • SOLiD import of paired-ends data improved. In some cases paired-ends data also contains single reads which are now removed during import.
  • Possible to import cas files created by the CLC NGS Cell (the command-line version of the assembly algorithms of the QIAGEN CLC Genomics Workbench)
  • Contigs can be exported in ACE format
  • Improvement of ACE file importer
  • Trim information in sff files can be used during import
  • Support for import of SCARF files (from Illumina Genome Analyzer systems)
  • Export of graph data points in csv format

Various high-throughput sequencing improvements

  • SNP detection now also reports position relative to the reference sequence as well as the consensus sequence. The table includes both positions per default (can be checked on and off), and the user decides where annotations should be added. Read more…
  • SNP detection table includes information about the name of annotations covering the SNPs. Previously only the annotation type was reported.
  • Trimming now also supports paired-ends data. If one of the reads in a pair is trimmed off, the whole pair will be removed.
  • Partially matched reads are reported as a graph along the contig.
  • Possibility to open consensus sequence with gaps. Right-click the label of the consensus sequence in the contig view and select: Open Copy of Sequence Including Gaps. The gaps will be represented by Ns in the new sequence.
  • Dynamic consensus graph removed from contig view. Since contigs now have a “real” consensus sequence which is also updated to reflect changes in the reads, the dynamic consensus sequence which is switched on in the Side Panel has been removed.
  • Annotations can be transferred from reference to consensus sequence in bulk. Right-click one of the annotations and choose “Copy to Consensus Sequence” or “Copy Annotations of Type xx to Consensus Sequence”.
  • Multiplexing now also possible for paired-end reads

Plug-in updates

  • New plug-in! GFF/GTF support: You can now annotate a sequence using a GFF/GTF file. The plug-in is available for all Workbenches (not CLC Sequence Viewer). Once installed, you find it in Toolbox->General Sequence Analysis-> Annotate from GFF/GTF File. Read more…
  • Extract annotations plug-in updated: it now uses the name of the annotation as the name of the new sequence.

Annotation handling

  • Annotation table has been greatly improved:
    • supports very long, heavily annotated genomes
    • usability of the filtering has been improved with feedback on the filtering process
  • Advanced renaming options. Read more…

Bug fixes

  • Fixed bugs related to contig editing.
  • Various bug-fixes.
  • Fixed problem with import in 2.0 release.


QIAGEN CLC Genomics Workbench 1.1.1

Release date: 2008-07-10

New features

  • Scrollbars can be adjusted manually

Problems fixed

  • Fixed problems when aligning sequences with lowercase characters
  • Fixed import of trace files without quality scores
  • Fixed problem when removing location
  • A new sequence list can be created from a selection in the table view
  • Better memory handling and managment of large contigs
  • User definable scrollbar areas for contig views
  • A few other minor bugs have been fixed.


QIAGEN CLC Genomics Workbench 1.1

Release date: 2008-06-27

New features

  • Increased speed of de novo assembly
  • Option of generating a contig table as a result of de novo assembly. This way the workspace is not polluted by a large number of contigs.
  • Multi contig table has options for opening contigs or extracting consensus sequences for further analysis
  • Much smoother scrolling on contigs when there is very high coverage

Problems fixed

  • Problems with import of .ACE files
  • Problems with excessive generation of files when doing de novo assembly of short read data
  • Problems with the use of quality scores in SNP detection