ABySS 1.3.1 (Oct 24, 2011)


Fix a bug in KAligner and fix a compiler error for Mac OS X.

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For all platforms (584 kB)

Debian package (amd64)

For Linux (1.4 MB)

Release Notes

State Final release
License BCCA (academic use)
Released 2011/10/24 00:00:00 GMT-7

This release fixes a bug in KAligner that caused values of k less than half the read length to fail and fixes a compiler error for Mac OS X. BWA-SW may be used for read alignments by setting aligner=bwasw, which is useful for long reads. When using abyss-map for alignments, a different value of k may be used for the read alignments than for the assembly by specifying ALIGNER_OPTIONS=-k##. The Sequence Read Archive (SRA) file format is supported provided that the tool fastq-dump from the sratoolkit is installed.

Change log

2011-10-24 Shaun Jackman <sjackman@bcgsc.ca>

* Read sequence files in SRA format. The tool fastq-dump from the
sratoolkit must be installed.
* Read a contig overlap graph in the ASQG format of SGA.
* Fix compile errors for Mac OS X.
* Fix the bug that caused the line number of an error in a FASTQ
file to be reported incorrectly.

* Support using BWA-SW to align reads to contigs by specifying
* The parameter ALIGNER_OPTIONS may be used to specify a different
value for k when aligning using abyss-map.
* New target, bam, may be used to produce a final BAM file of the
reads aligned to the scaffolds.

* Fix the bug causing the error:
Assertion `qstep >= 0 && qstep <= m_hashSize' failed.

* The result is independent of the order in which the mate-pair
libraries are specified.
* Permit scaffolding contigs that have non-numeric identifiers.
* The overlap graph is optional.

* Convert adj, dist or ASQG formatted graph files to dot format.
* Merge multiple graph files into one.