ABySS 1.2.6 (Feb 07, 2011)

Sequence variants are popped if the two variants are at least 90% similar. Contigs that overlap by fewer than k-1 bp are found and may be merged.

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

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Release Notes

2011-02-07  Shaun Jackman  <sjackman@bcgsc.ca>

    * Release version 1.2.6.
    * Find contigs that overlap by fewer than k-1 bp.
    * Pop bubbles with sufficient sequence identity.
    * Merge paths that overlap unambiguously.

    abyss-pe:
    * New parameter, m, the minimum number of overlapping bases.
    The default is 30.
    * The minimum sequence identity parameter, p, applies to both
    PopBubbles and PathConsensus.

    ABYSS:
    * Support values of k larger than 96. The maximum value of k is
    set when compiling using `configure --enable-maxk´.

    AdjList:
    * Find sequences that overlap by fewer than k-1 bp. The parameter
    m specifies the minimum number of overlapping bases.

    PopBubbles:
    * Align both branches of the bubble and pop bubbles whose sequence
    identity is sufficient, at least 90% by default.
    * New parameter, p, the minimum identity required.
    * The maximum bubble size is unlimited by default. This limit can
    be changed using the parameter b.

    SimpleGraph:
    * Extend each path as long as is unambiguously possible.

    PathOverlap:
    * Merge paths that overlap unambiguously.

    MergeContigs:
    * Perform an alignment of the two sequences when no simple overlap
    is found.

    abyss-fac:
    * New option, -g. Specify the expected genome size.