ABySS 1.2.7 (Apr 15, 2011)

Support using bwa or bowtie to align reads to contigs. New parameter, d, to specify the acceptable error of a distance estimate.

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Release Notes

2011-04-15  Shaun Jackman  <sjackman@bcgsc.ca>

* Release version 1.2.7.

abyss-pe:
* Support using bwa or bowtie to align reads to contigs.
Specify aligner=bwa or aligner=bowtie.
* Integrate with IBM LoadLeveler.

PopBubbles:
* Use an affine gap penalty.
* The default maximum bubble length is 10 kbp.
* New option, --scaffold. Scaffold over bubbles with insufficient
sequence identity to be popped.

SimpleGraph:
* New parameter d to specify the acceptable error of a distance
estimate. The default is 6 bp.

PathConsensus:
* Use an affine gap penalty.

MergePaths:
* Fix a bug that causes PathOverlap to die with the error:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.