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Latest Improvements for QIAGEN CLC Genome Finishing Module


QIAGEN CLC Genome Finishing Module 20.0

Released on December 11, 2019 Updated to be compatible with with CLC Genomics Workbench 20 and CLC Genomics Server 20.

Improvements

The Join Contigs tool can now be linked to the Add Read to Contigs tool in workflows.

QIAGEN CLC Genome Finishing Module 1.9

Released on November 28, 2018 Updated to be compatible with with QIAGEN CLC Genomics Workbench 12 and CLC Genomics Server 11.

QIAGEN CLC Genome Finishing Module 1.8

Released on November 28, 2017
  • Fixed a bug causing the Annotate from Reference tool to throw an exception in rare cases.
  • Fixed a bug that caused the Annotate from Reference tool to incorrectly translate multi-interval annotations (e.g. CDS, mRNA) when target contigs matched the reference in the reverse orientation.
  • Fixed a bug that created a duplicate annotation when using the Annotate from Reference tool in some cases.
  • Fixed a bug that caused the Join Contigs tool to fail in rare cases.
  • 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.

QIAGEN CLC Genome Finishing Module 1.7.1

Released on December 5, 2017

Bug fixes

  • Fixed two bugs causing the Annotate from Reference tool to throw an exception in rare cases.
  • Fixed a bug that caused the Annotate from Reference tool to incorrectly translate multi-interval annotations (e.g., CDS, mRNA) when target contigs matched the reference in the reverse orientation.
  • Fixed a bug that created a duplicate annotation when using the Annotate from Reference tool.
  • Fixed a bug that caused the Join Contigs tool to fail in rare cases.

QIAGEN CLC Genome Finishing Module 1.7

Released on March 2nd, 2017

Improvement

  • The Analyze Contigs tool now supports circular genomes. The parameter "Minimum distance to contig ends" no longer affects circular genomes.
  • Made the Annotate from Reference tool not transfer protein translations by default and added an option to force translations to be transferred.

Bug fix

  • Fixed a bug that occasionally caused an error when splitting contigs.
  • Fixed a bug that occasionally made the Correct Pacbio Reads tool crash or freeze when run with many threads.

QIAGEN CLC Genome Finishing Module 1.6.4

Released on December 5, 2017

Bug fixes

  • Fixed two bugs causing the Annotate from Reference tool to throw an exception in rare cases.
  • Fixed a bug that caused the Annotate from Reference tool to incorrectly translate multi-interval annotations (e.g., CDS, mRNA) when target contigs matched the reference in the reverse orientation.
  • Fixed a bug that created a duplicate annotation when using the Annotate from Reference tool.
  • Fixed a bug that caused the Join Contigs tool to fail in rare cases.

QIAGEN CLC Genome Finishing Module 1.6.3

Released on March 6, 2017

Improvements

  • The Analyze Contigs tool now supports circular genomes. The parameter "Minimum distance to contig ends" no longer affects circular genomes.
  • Made the Annotate from Reference tool not transfer protein translations by default and added an option to force translations to be transferred.

Bug fixes

  • Fixed a bug that occasionally caused an error when splitting contigs.
  • Fixed a bug that occasionally made the Correct Pacbio Reads tool crash or freeze when run with many threads.

QIAGEN CLC Genome Finishing Module 1.6.2

Released on July 21st, 2016

Bug fix

  • Fixed a bug in the Correct PacBio Reads tool that caused the tool to crash when run on a machine without SSE3 support.

QIAGEN CLC Genome Finishing Module 1.5.3

Released on June 1st, 2016

Improvement

  • Improved both running time and output quality of the “De Novo Assemble PacBio Reads” tool.
  • Improved manual entry for the “Correct PacBio Reads” and “De Novo Assemble PacBio Reads” tools.
  • Unlocked the “Coverage percentage of reads to correct” option of the “Correct PacBio Reads” tool in the “PacBio De Novo Assembly Pipeline” workflow.
  • Added a parameter, “Minimum anchor length”, to the “De Novo Assemble PacBio Reads” tool. Please see the manual for a description of this parameter.
  • Changed the input of the ”PacBio De Novo Assembly Pipeline” workflow from “Raw PacBio Importer” to an ordinary “Workflow input”.
  • Changed the default value of the “Contig polishing” option in the “De Novo Assemble PacBio Reads” tool to “Contig polishing using separate reads”.

Bug fix

  • Fixed a bug that made the manual entry for the “PacBio De Novo Assembly Pipeline” workflow inaccessible from the workflow itself.

QIAGEN CLC Genome Finishing Module 1.6.0

Released on March 31, 2016 Released to ensure compatibility with QIAGEN CLC Genomics Workbench 9.0 and Biomedical Genomics Workbench 3.0

QIAGEN CLC Genome Finishing Module 1.5.2

Released on November 12, 2015

Improvements

  • In the Add Reads to Contigs tool, affine gap cost parameters are now disabled when linear indel mode is selected, and vice versa.

Bug fixes

  • Fixed a bug that caused the ‘Annotate From Reference’ tool to fail when the ‘Add annotations to aligned contigs’ option was selected together with at least one of the options ‘Create table of transferred annotations’ or ‘Create table of annotations not transferred’.
  • Corrected invalid ‘Aligned sequences’ output in the Annotate from Reference tool that occurred when the tool was used in a workflow and both the ‘Aligned sequences’ and ‘Annotated contigs’ output options were enabled.
  • Fixed a bug that caused the Add Reads to Contigs tool to fail when no reads map to the contigs.

QIAGEN CLC Genome Finishing Module 1.5.1

Released on August 20, 2015

New features

  • Error correction and de novo assembly of PacBio long reads (beta)

Improvements

  • Added an output option in the Annotate From Reference tool to create contigs with annotations
  • The PacBio importer now also accepts FASTA files as input
  • Enabled import of PacBio reads to Genomics Server from local files

Bug fixes

  • Fixed the link to the Genome Finishing Module help in the help menu
  • Fixed import of PacBio reads to server from local files
  • Fixed a bug that occurred when selecting a row in a Contig Match Table corresponding to a contig that had previously been filtered out in the Contig Table
  • Fixed a rare bug that caused an error when updating the user interface after two contigs were joined manually

Changes

  • Adding long read support for QIAGEN CLC Genome Finishing Module: PacBio long read error correction and de novo assembly functionality is added (beta)

QIAGEN CLC Microbial Genome Finishing Module 1.4

Released on August 28, 2014

Changes

  • The tool “Sample reads” is now a part of the genomics workbench and has been removed from the module.
  • Join Contigs is out of beta.

Improvements

  • Minor quality improvements for the long read scaffolding option in Join Contigs.

QIAGEN CLC Microbial Genome Finishing Module 1.3.3

Released on July 4, 2014

Bug fixes

  • Fixed bug in Align Contigs when some references had no contigs matching.
  • Fixed bug in Align Contigs when splitting a contig leading to one of the contigs not having any reads afterwards.

QIAGEN CLC Microbial Genome Finishing Module 1.3.2

Released on March 19, 2014

Bug fixes

  • Fixed a compatibility issue in the Align Contigs tool which caused errors when modifying contigs.
  • Fixed a bug that caused the Join Contigs (beta) tool to crash when performing reference based scaffolding where one or more references had less than one contig aligned.
  • Fixed splitting contigs when using the contigs as reference.

QIAGEN CLC Microbial Genome Finishing Module 1.3.1

Released on March 12, 2014
Compatibility release

QIAGEN CLC Microbial Genome Finishing Module 1.3.0

Released on January 30, 2014

New features

  • Support for scaffolding with long reads, such as PacBio reads, in the Join Contigs tool.
  • Importer for PacBio reads
  • Support for sequencing primers in the Create Primers tool.

Improvements

  • The Join Contigs tool now supports joining multiple contigs into one.
  • Improved handling of repeats in the Join Contigs tool.
  • Improved performance of the Join Contigs tool when using reference sequences for joining.

Bug fixes

  • Fixed a bug in the Create Primers tool which caused the “Minimum distance to annotation” to be ignored in some cases.

QIAGEN CLC Microbial Genome Finishing Module 1.2.1

Released on September 18, 2013

Bug fixes

  • Fixed a problem in Join Contigs (beta) when two contigs overlapped by more than the smallest of the contig lengths.
  • Removed unnecessary restriction on different input types in Align Contigs.
  • Find Sequence now correctly finds multiple hits in each sequence.
  • Fixed a bug that occured when joining reversed contigs in the Align Contigs editor and resulted in incorrect joins.

QIAGEN CLC Microbial Genome Finishing Module 1.2.0

Released on August 29, 2013

New features

  • New tool for transferring annotations from references to contigs.
  • All tools (not in beta) have been workflow-enabled.

Improvements

  • Sample reads: The method of picking reads has been redesigned. Now the reads are picked at random rather than with a regular frequency.
  • Extend Contigs has a new parameter allowing to specify the fraction of unaligned ends allowed in the extension before not extending any further.
  • The Analyze Contigs tool can now generate a report with statistics on the problems that were identified.
  • The speed of the Create Primers tool has been significantly improved when “exact matching” is used to check for mispriming.
  • Join Contigs tool now outputs a table of the joins performed.

Changes

  • Add Reads to Contigs no longer updates the contigs based on the final mapping.

Bug fixes

  • The allowed merge distance between matches of contigs in Align Contigs only in the reference, and not also the contig, was considered.
  • When contigs were edited in Align Contigs but the mapping wasn’t updated, saving and reopening didn’t allow the matches to be updated any longer.
  • Selections made in Align Contigs results now shows the correct text rather than being overriden by other selection texts.

QIAGEN CLC Microbial Genome Finishing Module 1.1

Released on May 21, 2013

New features

  • Added the “Join Contigs” tool which is a tool that can automatic join contigs based on three types of informations: Overlaps between contigs; paired information; alignment to a releated reference.
  • Improved detection of overlaps between contigs when the contigs themselves are used as reference in the “Align Contigs” tool. This has been achieved by increasing the sensitivity of the overlap detection in the contig ends.
  • The amplicon creator is now able to filter annotation using qualifier/key values.
  • Made it possible to select a subset of paired libraries in the “collect paired read statistics” tool.
  • Included a tool for removing extentions of contig ends that haven’t been used for joining two contigs.
  • Added a copy button to the “Align Contigs” tool which can be used to make a copy of a contig.
  • Added a “minimum coverage” parameter to the unaligned ends detection in the “analyze contigs” tool.
  • The default parameters of the “Create Primers” tool have been updated.
  • The “Create Amplicon” tool can now create amplicons with a negative overlap, i.e. amplicons separated by gaps.
  • Option for G/C anchors in the Create Primers tool.

Bug fixes

  • Fixed a bug which caused contigs to be incorrectly orientated when using the manual join function in the “Align Contigs” tool.
  • Fixed a bug which caused non-existing annotation to appear in the “Create Primers” wizard.
  • Fixed several bugs concerning selection of regions in the “Align Contigs” tool. The synchronization of selections in tables and the match view is now faster.
  • Fixed a bug which could cause an error when refreshing the match view after a contig had been modified.
  • All actions in the “Align Contigs” tool can now be stopped.
  • Annotations when joining contigs are now transferred correctly

QIAGEN CLC Microbial Genome Finishing Module 1.0.2

Released on April 30, 2013

Improvements

  • Fixed manual join in Align Contigs.
  • Fixed potential problem in update after manual edit of contigs in Align Contigs.

QIAGEN CLC Microbial Genome Finishing Module 1.0.1

Improvements

  • In the Align Contigs table, the column “Contig match length” has been renamed to “Contig span length” and the default status of the column has been changed to hidden to avoid confusion with the “Aligned nucleotides” column.
  • Fixed bug where contigs exported from the Contig Aligner could not be used as input to the read mapper.
  • Fixed several issues with the Reassembly Regions tool, which could cause the tool to crash or contigs to disappear after reassembly.
  • Fixed bug in the progress bar of the Analyse Contigs tool.
  • The Create Primers tool now checks for mispriming on all input sequences instead of just the target sequence.
  • Primer melting temperatures are now output with two decimals instead of 15.
  • Fixed a bug which caused the synchronization of selections in the Contig Aligner to break when a contig had no reads aligned.
  • The history of the Add Reads to Contigs tool now contains the number of reads that were successfully mapped to contigs.
  • The history of the Analyze Contigs tool now states the input objects.
  • Fixed an issue which prevented the user from updating contig matches in the contig aligner although this was necessary.
  • Removed the open/save dialog from the Reassemble Regions tool when the tool is activated through the right click menu.
  • Help in the Align Contigs tables is now working.
  • Fixed a few problems with selections in the Align Contigs tool concerning merged regions of contig matches.

QIAGEN CLC Microbial Genome Finishing Module 1.0

Improvements

  • The “Align Contigs” tool now accepts contigs imported with the FASTA and Sanger importers.
  • Added an option for the minimum number of reads required in the “Extend Contigs” tool.
  • Minor bug fixes in the “Extend Contigs” and “Align Contigs” tools.