Latest improvements for CLC Genomics Server

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CLC Genomics Server 10.0.0

Release date: 2017-11-21

Server specific

Improvements and new features

  • "Output file from CL" in External Applications (EA) configurations now supports the configuration of parameters for exporters. Existing EA configurations will continue to work using the older configuration, exactly as on older versions of the CLC Genomics Server. Only if a change is made, and saved, to an existing configuration of an "Output file from CL" entry, will the exporter be updated to support the configuration of parameters.
  • The report generated by the "check setup" functionality now lists information about the installed licenses.
  • External Applications can now be organized into subfolders of the External Applications area of the Workbench Toolbox.
  • The time needed to complete the "Saving results" step of a workflow running on a CLC Genomics Server has been shortened.
  • The column headings in the table containing statistics for each mapping, optionally produced by the QC for Read Mapping Tool (Bx-enabled servers only) and the Create Detailed Mapping Report tool, have been made more descriptive.
  • Fixed an issue where the removal of terminated sub batch-processes from the Workbench Processes tab before the master process finished would produce an error dialog.
  • 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 and for Bx-enabled Servers, Add Fold Changes and Add Information from Overlapping Variants.

Bug fixes

  • An issue was fixed that caused a Workbench restart to be necessary for running an External Application if it had been changed on the CLC Genomics Server since the time the Workbench user had logged into that server.
  • Fixed an issue where only one post-processing step in an External Application configuration was listed next to an "Output file from CL" parameter, even when multiple post-processing steps had been linked to it.
  • Fixed an issue where export to CLC or zip format led to an error when permissions were set on both the source CLC Genomics Server file location and also on the Import/Export location the data was to be exported to.
  • Fixed an issue affecting unknown users trying to log into the CLC Genomics Server where the server was incorrectly configured with LDAP with Bind DN while pointing towards an Active Directory (AD) backend. Such logins will now fail. Previously an anonymous login would result.

Shared with workbenches

Improvements and new features

  • Trim Reads:
    • The Trim Sequences tool 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. For a Biomedical-enabled server, this change also affects the inbuilt workflow Prepare Raw Data.
  • 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.
  • 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.
  • 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 history of a data element can now be exported as a CSV format file.
  • 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%.
  • The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of the CLC Genomics Server, so the version available for download could change over time from the one recorded here.
  • Clicking "Select genes in other views" in a Volcano Plot with an empty selection no longer gives an error message.
  • When exporting files to SAM or BAM format files, information is now entered into the optional fields NM (edit distance) and MD (mismatch string).
  • 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.
  • NCBI blast executables are upgraded to version 2.6.0.
  • 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.
  • Parameters for the Trim Sequences tool are now shown in the same order when running the tool from the Toolbox or within a workflow.
  • 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.


  • The Roche 454 and SOLiD Import tools have been moved to the Legacy folder of the Workbench Toolbox. These will be retired in a future release.
  • 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 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.
  • 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.
  • The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.

Bug fixes

  • 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 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 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 CLC Genomics Server, 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.
  • 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 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 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.
  • Fixed an issue with the QC for Target Sequencing tool (Bx-enabled servers only) and 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 with the Add Information about Amino Acid Changes tool (Bx-enabled servers only) and 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 (Bx-enabled servers only) and 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.

Plugin Notes for Biomedical-enabled server

  • A new plugin, QIAseq Targeted Panel Analysis 1.0, unifies the three QIAseq Targeted Panel plugins that were previously available: QIAseq DNA V3 Panel Analysis, QIAseq Targeted RNA Panel Analysis and QIAseq Targeted RNAscan Panel Analysis. The new plugin covers Targeted DNA for variant calling, Targeted RNA for differential expression and Targeted RNAscan for fusion gene detection with improvements resulting in more accurate variant calling and fusion gene detection.


The follow software are the corresponding clients for the CLC Genomics Server 10.0
      • CLC Genomics Workbench 11.0
      • Biomedical Genomics Workbench 5.0 (when the server has the Biomedical Extension)
      • CLC Command Line Tools 5.0

Advanced notice

The following will be retired and will not be available in the the next major release of the software:
  • SOLiD colorspace data support, including import
  • The Roche 454 NGS import tool
If you are concerned about the proposed changes, please contact our Support team ([email protected]).

CLC Server Command Line Tools

Changes to existing tools

export -e fastq
  • The default behavior of this tool has changed To maintain current behavior, scripts using this exporter must have "--export-paired-reads-to-two-files false  --one-file true" added to the command. 
  • --export-paired-reads-to-two-files" has been added. This parameter is set to true by default.
  • The default value of the --onefile parameter has been changed from true to false.  Note that the --onefile parameter cannot be set to true when the --export-paired-reads-to-two-files parameter is also set to true.  Having both set to true will cause the tool to fail with an error.
  • -e gcg                       has been removed.  Export to gcg format is no longer available
    •  --include-partially-covering-reads   has been added. When set to true, reads that partially cover variants will be included when calculating the results, enabling detection of variants longer than the reads. Set to false by default.
    •  The default behavior of this tool has changed To maintain current behavior, scripts must have " --readthrough-trimming false" added to the command.
    • --readthrough-trimming   has been added. Detects overlaps in paired reads and trims the non-overlapping part away.
    •  --reverse-strand     has been removed.  This option is no longer used nor recognized. The default value in earlier versions was false.
  •  The default behavior of this tool has changed To maintain current behavior, scripts must have " --readthrough-trimming false" added to the command.
  •  --readthrough-trimming  has been added and the default is set to true.   
  • --reverse-strand     has been removed. This option is no longer used nor recognized. The default value in earlier versions was false.

New features

  • -e history_csv           Export of history information to csv format has been added.

Advanced Notice

The NGS import tools ngs_import_roche454 and ngs_import_solid will be retired and will not be available in the the next major release of the software.  

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