Latest improvements for CLC Genomics Server

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CLC Genomics Server 9.1.1

Release date: 2017-06-22

Bug fixes

  • Fixed an issue introduced in CLC Genomics Server 8.5 causing the Merge Annotation Tracks tool to fail when used on tracks with more than 6 chromosomes.
  • Fixed an issue introduced in the Biomedical enabled CLC Genomics Server 9.1 where workflows containing the Copy Number Variant Detection tool could not be updated automatically. (Biomedical-enabled servers only)

Compatibility

The following are the corresponding clients for the CLC Genomics Server 9.1.1

  • CLC Genomics Workbench 10.1.1
  • Biomedical Genomics Workbench 4.1.1
  • CLC Command Line Tools 4.1.1

We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 10.0.0, 10.0.1 and 10.1, Biomedical Genomics Workbench 4.0 and 4.1, and CLC Command Line Tools 4.0 and 4.1 can connect to CLC Genomics Server 9.1.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

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 ([email protected]).

 

 

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 9.1.1.

Compatibility

CLC Command Line Tools 4.1.1 is the corresponding client for CLC Genomics Server 9.1.1.

CLC Command Line Tools 4.1.1 can also act as a client for the CLC Genomics Server 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server. 



CLC Genomics Server 9.1.0

Release date: 2017-06-15

Server specific

  • Improved messaging in the web administrative interface when workflows installed on the server have unresolved dependencies, such as missing plugins, licenses or data.
  • More detailed feedback is now presented in the Plugins tab of the web administrative client when there are issues with installed plugins, such as missing or expired licenses or version incompatibilities.
  • Fixed a connection issue with LDAP authentication over SSL when the "Disable SSL certificate check" setting was used. This problem was introduced in CLC Genomics Server 9.0.

Shared with workbenches

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 DetectionLow 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 the GFF3 Exporter could generate invalid GFF3 for features of length 0.

Shared with Biomedical enabled Genomics Server only

  • Fixed a bug in the Copy Number Variation Detection tool where the target-level output could not be produced unless a gene track was also specified.
  • Fixed an issue in the Copy Number Variation Detection tool where the data in the "Fold-change (adjusted)" and "Fold-change (raw)" columns were reversed in the target-level CNV output.

Compatibility

The following are the corresponding clients for the CLC Genomics Server 9.1.0

  • CLC Genomics Workbench 10.1.0
  • Biomedical Genomics Workbench 4.1.0
  • CLC Command Line Tools 4.1.0

We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 10.0.0 and 10.0.1, Biomedical Genomics Workbench 4.0, and CLC Command Line Tools 4.0 can connect to CLC Genomics Server 9.1.0. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

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 ([email protected]).

 

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 9.1.0

 

Compatibility

 

CLC Command Line Tools 4.1.0 is the corresponding client for CLC Genomics Server 9.1.0.

 

CLC Command Line Tools 4.1.0 can also act as a client for the CLC Genomics Server 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server. 



CLC Genomics Server 9.0

Release date: 2017-03-02

Server specific

New features and improvements

  • The tabs "Import", "Export" and "Sequence Text" have been removed from the web administration interface. Viewing, import and export functionality are available via Workbench clients, and import and export functionality is also available using the CLC Command Line Tools client.
  • 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.
  • Temporary *.cpw files are now deleted immediately after installation of server workflows from the workbench. Previously these were deleted later, when the finished server process for the installation was removed.
  • Various minor improvements

Bug fixes

  • Fixed a problem where permission changes were not applied as expected when using the  "Apply to all subfolders" option when setting group permissions on a folder in server data locations.
  • Fixed an issue where the CLC Genomics Server would wait indefinitely when there was a stalled connection to the LDAP server.
  • Fixed an issue that caused the import of Wiggle and USCS chromosome band files to fail on CLC Genomics Server setups.
  • Fixed an issue where batch jobs submitted to the CLC Genomics Server would not always display all the sub-processes in the Processes tab in a Workbench.
  • Various minor bugfixes.
 

Shared with workbenches

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. 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 (for CLC Genomics Server)  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 in this column.

Import/Export

  • A tool to import PacBio data is now available. It is located at Import | PacBio  in Workbenches.
  • 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 speed of importing to tracks where the original file contains data relating to many chromosomes has been substantially improved.
  • 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.

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 used as part of Map Reads to References and the Map Reads to Contigs tools has been updated. The update includes improved read mapping quality for longer reads, improved memory performance for the index building stage, as well as 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.
  • Options to search the full text or abstracts available in Pubmed have been added to the Search for Reads in SRA tool
  • 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.
  • 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 CLC Genomics Server 9.0, indices for the locations containing the relevant data will need to be rebuilt.
  • 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, which sometimes reported incorrect read counts for circular sequences.
  • Fixed an issue where the Basic Variant DetectionLow 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 GenBank and EMBL exports where quoting specifications were not being conformed to.
  • Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
  • The speed of sorting and loading tracks in the Workbenches has been greatly improved. Due to these changes, tracks created with this version of the CLC Genomics Server and later ones cannot be used in older Workbenches or Servers. Backwards compatibility has been maintained: tracks created using older versions of the Workbench or CLC Genomics Server can continue to be used.
  • Various minor bugfixes.

Shared with Biomedical enabled Genomics Server only

  • Two new human reference data sets are available for download from the Reference Data Manager. One is based on Ensembl 86 and the other is based on RefSeq GRCh38.p9.
  • The three workflows Identify and Annotate Differentially Expressed Genes and Pathways for human, mouse, and rat have been replaced by three new workflows of the same names. The new workflows benefit from the inclusion of new RNA-seq tools.
  • The Ready-to-use workflows listed under the "Whole Transcriptome Sequencing" folder of the Workbench Toolbox now support strand-specific RNA-seq protocols by allowing the "Strand Specific" parameter to be set.
  • In all Ready-to-Use workflows containing the tool Map Reads to Reference, the default value for the parameter "Cost of insertions and deletions" has been changed to "affine" (it used to be "linear"). Default values have not been changed in the case where the tool is launched directly.
  • Less temporary space is now consumed when downloading data via the Reference Data Manager.
  • 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 tool Identify Differentially Expressed Gene Groups and Pathways.
  • Fixed a bug in the Create Detailed Mapping Report (or QC for Read Mapping tool in Biomedical enabled Genomics Server), which sometimes reported incorrect read counts for circular sequences.

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.
  • The tool Trim Primers of Mapped Reads has been retired. For trimming primers from mapped reads, please use the Trim Primers and their Dimers from Mapping tool, which is distributed with the QIAGEN GeneRead Panel Analysis Server Plugin.
 

Compatibility

The follow software are the corresponding clients for the CLC Genomics Server 9.0
      • CLC Genomics Workbench 10.0
      • Biomedical Genomics Workbench 4.0 (when the server has the Biomedical Extension)
      • CLC Command Line Tools 4.0

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 section for more details.

CLC Server Command Line Tools

All CLC Genomics Servers

New Tools
RNA-seq related
  • create_combined_rnaseq_report        Create Combined RNA-Seq Report
  •  create_expression_browser               Create Expression Browser
  •  create_heatmap_for_rnaseq              Create Heatmap fo RNA-Seq
  •  create_venn_diagram_for_rnaseq     Create Venn Diagram for RNA-Seq
  •  differential_expression_rna_seq        Differential Expression for RNA-Seq
  •  gene_set_test                                    Gene Set Test
  •  principal_component_for_rna_seq     PCA for RNA-Seq
  •  spikein_control_import                       RNA Spike-ins
Other tools
  • -e gff3     export to gff3 format
Improvements
  • Help for the CLC Command Line Tool is no longer printed to the console when errors are returned.
Changes
Commands removed
  •  probabilistic_variant_detection       Probabilistic Variant Detection. Legacy tool, now retired.
  • quality-based_variant_detection     Quality based Variant Detection. Legacy tool, now retired.
  • -e gff     export to gff.  Use the new gff3 exporter instead.
Options added to commands

rna_seq

  • --spike-in-settings                         Map reads to spike-in controls (default: NONE)
  • --spikein-controls                          Select spike-in controls
exporting to bam format  (-A export -e bam)
  • --index <Boolean>                        Create an index file (.bai) (default: false)
Options removed from commands

rna_seq

    •  --em-enabled
    • --mapping-type
The tool now runs with EM enabled by default.

sequencing_qc_report

    • --include-overrepresentation-analysis
    • --include-quality-score-analysis
The tool now generates these outputs as part of the report by default.

Biomedical Enabled CLC Genomics Servers only

Changes in addition to those listed for all CLC Genomics Servers
Options removed from commands

qc_for_sequencing_reads

    • --include-overrepresentation-analysis
    • --include-quality-score-analysis
 


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