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@traymond traymond released this 11 Dec 22:22
· 1527 commits to master since this release

Summary

Scaffolds can now be rescaffolded using long sequences such as RNA-Seq assemblies produced from Trans-ABySS. Added support for gcc 4.8+ and Mac OS X 10.9 Mavericks with clang. Finally, we've licensed ABySS under GPL for non-commercial purposes. Please read the LICENSE file for more details.

ChangeLog

2013-11-20 Anthony Raymond [email protected]

  • Release version 1.3.7
  • Use long sequences to rescaffold scaffolds. May be run by
    adding libraries to the `long’ parameter. When Scaffolding
    with RNA-Seq contigs from a Trans-ABySS assembly, the genic
    contiguity is greatly improved.
  • Added support gcc 4.8+, and Mac OS X 10.9 Mavericks with clang.
  • Licensed as GPL for non-commercial purposes.

abyss-fac:

  • Added e-size to contiguity statistics as described in the GAGE
    paper.

abyss-filtergraph:

  • Bug fix. `--assemble’ will not fail an assertion.
  • New option, --max-length, used to remove contigs over the
    specified threshold.
  • Trim 2-in 0-out tips when removing tips.

abyss-map:

  • Bug fix. Correctly set mapq=0 for reads that multi map.

abyss-longseqdist:

  • New program. Generate distance estimates between all contigs a
    single read maps to.

abyss-mergepairs:

  • Report number of reads chastity filtered.

abyss-overlap:

  • Bug fix. Handle ambiguity codes.

abyss-pe:

  • Support BWA-MEM with assembly. Run using parameter
    `aligner=bwamem’.
  • Added another scaffolding stage using long sequences. May be
    run by adding libraries to the `long’ parameter.

ABYSS-P:

  • Bug fix. Do not use awk to merge fasta files.

abyss-samtobreak:

  • Building bug fix. Check that ghc modules are installed.

UnitTest:

  • The Google C++ testing framework has been added to ABySS.