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Latest improvements for QIAGEN CLC Assembly Cell

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QIAGEN CLC Assembly Cell 5.1.1

Release date: 2018-11-14

Bugs

  • Fixed a bug in 'clc_mapper' that led to some deletions being reported as multiple, separate deletions instead of a single, larger deletion, when affine gap costs were used.

Advanced notice

The tools 'clc_mapper_legacy' and 'clc_remove_duplicates' will be retired starting from Assembly Cell 6.0 onward. They will remain present on older release lines. If you are concerned about the proposed changes, please contact our Support team ts-bioinformatics@qiagen.com


QIAGEN CLC Assembly Cell 5.1

Release date: 2018-04-05

Improvements

  • Added a new parameter --normaltypelimit (-S) to 'clc_mapper' for specifying the read length to be applied when deciding when to switch to long read mapping. The default value is 500 (bp), which guarantees the same default behavior as the previous version (Assembly Cell 5.0.5).
  • Added a new parameter --mappermemory (-M) to 'clc_mapper' that allows the amount of memory (MB) to be used during mapping to be restricted. This parameter needs to be set when --normaltypelimit (-S) is used, since the memory usage increases with the squared read length, which can potentially cause the system to run out of memory. The -M parameter overrides the --cpus parameter to ensure a lower memory usage.

Bugs

  • Fixed a very rare bug in 'clc_mapper', where an alignment with a leading unaligned end could result in a wrong score
  • Fixed  a bug where 'clc_correct_pacbio_reads' would segfault if not given an output file
  • Fixed a bug where the argument --interleave was not accepted by the tool 'clc_quality_trim' 

Changes

  • 32 bit versions of the QIAGEN CLC Assembly Cell are no longer distributed.

Advanced notice

The tools 'clc_mapper_legacy' and 'clc_remove_duplicates' will be retired starting from Assembly Cell 6.0 onward. They will remain present on older release lines. If you are concerned about the proposed changes, please contact our Support team ts-bioinformatics@qiagen.com


QIAGEN CLC Assembly Cell 5.0.5

Release date: 2017-11-08

Bugs

  • Fixed a very rare issue, where a read could be aligned incorrectly and would be reported as not mapped.

Advanced notice

From the next feature release of QIAGEN CLC Assembly Cell and forward, 32 bit versions of the QIAGEN CLC Assembly Cell will no longer be distributed.


QIAGEN CLC Assembly Cell 5.0.4

Release date: 2017-06-21

Bugs

  • Fixed an issue in the clc_mapper tool where length and similarity fraction cut-offs were ignored for reads where the best read alignment was a stretch of exact matches, with no extension from that seed possible, and where the read was longer than 500bp.
  • Fixed an issue in the clc_mapper tool that caused it to crash if a sequence with length 0 was included in the reference set.

Advanced notice

From the next feature release of QIAGEN CLC Assembly Cell and forward, 32 bit versions of the QIAGEN CLC Assembly Cell will no longer be distributed.


QIAGEN CLC Assembly Cell 5.0.3

Release date: 2017-03-08

Bugs

  • Fixed a bug in the read mapper causing it to fail on CPUs with no support for SSSE3.
  • Fixed a bug that sometimes made the index building phase of the read mapper crash or freeze when run with many references and many threads.

Advanced Notice

From the next feature release of QIAGEN CLC Assembly Cell and forward, 32 bit versions of the QIAGEN CLC Assembly Cell will no longer be distributed.


QIAGEN CLC Assembly Cell 5.0.2

Release date: 2016-12-08

Improvements

  • The maximum memory requirement for read mapper index building has been decreased from three quarters to half of the physical memory.
  • Minor improvements to alignment quality of read mapping.

Bug fixes

  • Fixed an issue where the distance between paired reads could be miscalculated after read mapping if one of the two reads had an unaligned end. This lead to some pairs erroneously being marked as broken.
  • Read mapper index building now takes account of the --cpus parameter.
  • Cas file output from read mapping now reports sequence circularity correctly.
  • Default values in the usage information for the clc_assembler_long parameters minimum contig length, minimum word coverage and minimum anchor length have been corrected.

Changes

  • Random sampling between equally scoring alignments produced by read mapping has been changed to better mimic the behaviour in Assembly Cell 4.4.

Advanced Notice

From the next feature release of QIAGEN CLC Assembly Cell and forward, 32 bit versions of the QIAGEN CLC Assembly Cell will no longer be distributed.