1.3.7
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.