ABySS 1.1.0 (Dec 21, 2009)

ABySS will expand tandem repeats when it is possible to determine the exact number of the repeat. The paired-end path-finding algorithm, SimpleGraph, is multithreaded. Fixed a bug in MergePaths that could misassemble repeats larger than the paired-end fragment size. The output format of AdjList, DistanceEst and SimpleGraph has changed.

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

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Release Notes

2009-12-18 Shaun Jackman <sjackman@bcgsc.ca>

* Release version 1.1.0.
* The output format of AdjList, DistanceEst and SimpleGraph has
changed.

ABYSS:
* New options, -q, --trim-quality. Trim bases from the ends of
reads whose quality is less than the specified threshold.
--standard-quality: zero quality is `!' (33)
default for FASTQ files
--illumina-quality: zero quality is `@' (64)
default for qseq and export files
Thanks to Tony Raymond.

SimpleGraph:
* Multithreaded. The -j, --threads option specifies the number of
threads to use.
* Expand tandem repeats when it is possible to determine the exact
number of the repeat.

MergePaths:
* Bug fix. A repeat that is larger than the fragment size could
be misassembled. Thanks to Tony Raymond.

abyss-pe:
* Determine the parameter j (number of threads) by finding the
number of slots allocated on the head node in the PE_HOSTFILE.
* Store the k-mer coverage histogram in coverage.hist.