ABySS 1.3.4 (May 30, 2012)


This release eliminates two sources of misassemblies, one in the path extension logic of SimpleGraph. Two, the default value of m, which is the minimum overlap required between two contigs to merge them, is increased from 30 to 50. This release also fixes various portability issues. A new script, abyss-fatoagp, is included to create an AGP file for GenBank submission.

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

Available downloads


For all platforms (626 kB)

Debian package (amd64)

For Linux (1.7 MB)

Test input data (paired end reads)

For all platforms (1.4 MB)

Release Notes

State Final release
License BCCA (academic use)

2012-05-30 Shaun Jackman <sjackman@bcgsc.ca>

* Release version 1.3.4.
* Do not extend paths, which can cause misassemblies.
* Increase the default value of m from 30 to 50.
* Various portability fixes.

* Increase the default value of m from 30 to 50 to reduce the
likelihood of misassemblies.
* Integrate with SLURM. Thanks to Timothy Carlson.

* Use CityHash64 rather than Bob Jenkins' hashlittle.

* Do not extend paths. Closes #8. Extending paths can cause
misassemblies when the de Bruijn graph is incomplete.

* Bug fix. Closes #6. Fix the bug causing the error:
Assertion `!m_ambig' failed.

* New script. Create a FASTA file of scaftigs and an AGP file.