ABySS 1.0.11 (Jul 21, 2009)

Assemble colour-space reads. Read files in qseq format. KAligner is multithreaded. Integrate with Sun Grid Engine (SGE). Prevent misassemblies mediated by tandem segmental duplications.

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

Available downloads

Source

For all platforms (220 kB)

Release Notes

2009-07-21 Shaun Jackman <sjackman@bcgsc.ca>

* 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)