ABySS 1.2.2 (Aug 25, 2010)

Merge contigs after popping bubbles. Handle multi-line FASTA sequences. Report the amount of memory used.

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

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Source

For all platforms (287 kB)

Release Notes

2010-08-25 Shaun Jackman <sjackman@bcgsc.ca>

• Release version 1.2.2.
• Merge contigs after popping bubbles.
• Handle multi-line FASTA sequences.
• Report the amount of memory used.
• Most tools can output their results in SAM format, including AdjList, KAligner, ParseAligns and PathOverlap.

abyss-pe

• New command, se-dot. Output a Graphviz dot file of the single-end assembly.

ABYSS

• Handle multi-line FASTA sequences.
• Report the amount of memory used.
• Improve error messages for incorrectly-formatted FASTA files.
• Bug fix. Improved handling of palindromes.

PopBubbles

• Merge contigs after popping bubbles.
• Bug fix. Do not pop bubbles resulting from palindromes.

KAligner

• Report the amount of memory used.
• New option, --sam. Output the alignments in SAM format.

ParseAligns, DistanceEst

• Bug fix. The CIGAR string was oriented with respect to the query rather than with respect to the target, which is standard.

AdjList, PathOverlap

• New option, --sam. Output the adjacency graph in SAM format.

abyss-fixmate

• New program. Similar to samtools fixmate, but does not require that the input be sorted by query ID, although it is faster if it is sorted.