ABySS 1.3.7 (Dec 11, 2013)


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.

For additional information about this project, please visit the overview page .

Available downloads


For all platforms (724.9 KB)

Test input data (paired end reads)

For all platforms (1.4 MB)

Change log

2013-11-20 Anthony Raymond <traymond@bcgsc.ca>

* 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.

* Added e-size to contiguity statistics as described in the GAGE

* 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.

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

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

* Report number of reads chastity filtered.

* Bug fix. Handle ambiguity codes.

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

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

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

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