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Releases: bcgsc/abyss

Release version 1.3.6

31 Jul 23:54
@traymond traymond
1.3.6
c1c45b5
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Release version 1.3.6

2013-07-15 Anthony Raymond [email protected]

* Release version 1.3.6
* Improved documentation for GitHub devs.
* ABYSS-P performance improvement.
* Various portability and bug fixes.

abyss-mergepairs:
* Fix program name.

abyss-fac:
* New option --exp-size to give the expected genome size needed
for NG50 calculation.
* New option --count-ambig include ambiguities in calculations.

ABYSS/ABYSS-P:
* Performance improvement. Runtime reduced by ~20%.
* Fix support for MPICH.

abyss-map:
* No longer require POPCNT instruction.
* New option --order to force output order the same as input.

abyss-filtergraph:
* New option --remove to remove specified contigs from graph.

PopBubbles:
* Bug fix. Setting branches > 2 will now work.

abyss-fixmate:
* Improved error when first and second read IDs do not match.
* New option --cov to compute and store the physical coverage in
a Wiggle file.

AdjIO:
* Bug fix for non-GCC compilers.
Assets 2

1.0.11

28 Nov 20:31
@jwcodee jwcodee
1.0.11
6877d91
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1.0.11
  • Release version 1.0.11.
  • Assemble colour-space reads. Read identifiers must be named with
    the suffixes F3 and R3.
  • Read files in qseq format. Thanks to Tony Raymond (tgr).
  • Prevent misassemblies mediated by tandem segmental duplications.
    A sequence XRRY, where R is a repeat sequence, could have been
    misassembled as XRY. (tgr)

abyss-pe:

  • Integrate with Sun Grid Engine (SGE). A parallel, paired-end
    assembly can be run with a single qsub command. The parameters
    lib, np and k default to the qsub environment variables JOB_NAME
    (qsub -N), NSLOTS (qsub -pe) and SGE_TASK_ID (qsub -t)
    respectively.
  • The .pair file, the largest intermediate file, is now gzipped.

ABYSS-P:

  • Bug fix. At k=19, k-mer would be distributed to even-numbered
    processes only.

KAligner:

  • Multithreaded. The -j, --threads option specifies the number of
    threads to use. The order in which the alignments are output will
    vary from run to run, but the alignments are deterministic and
    will not vary. Each thread reads and aligns one file, so the reads
    must be in more than one file to use this feature. (tgr)
Assets 2