ABySS 1.0.15 (Oct 19, 2009)


New parameters, e and E, to set the coverage threshold of the erosion algorithm. Values for the parameters e and the coverage threshold, c, will be chosen automatically if they're not specified. The read length is now an optional parameter. Two important bug fixes, see below.

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Release Notes

State Final release
License AFL

2009-10-19 Shaun Jackman <sjackman@bcgsc.ca>

* Release version 1.0.15.

* New options, -e, --erode and -E, --erode-strand.
The parameter e erodes bases at the ends of blunt contigs with
coverage less than the specified threshold.
The parameter E erodes bases at the ends of blunt contigs with
coverage less than the specified threshold on either strand.
* New feature. If the parameters e and c are not specified,
attempt to choose appropriate values based on the observed k-mer
coverage. This feature will work best for higher coverage data.
For lower coverage data, setting e=c=2 is reasonable.
* New option, --trim-masked. Removed masked (lower case) sequence
at the beginning and end of the read. Disable with
* The read length, l, is an optional parameter. If the read length
is specified, the trim parameter, t, will default to 6*(l-k+1), as
before. If the read length is not specified, t will be set to the
same value as k. For longer reads or when k is less than 85% of l,
it should not be necessary to specify l. The parameter t may be
specified directly if desired.

* Bug fix. The standard deviation could be calculated incorrectly
for larger numbers, particularly for libraries with large fragment
sizes. Thanks to Tony Raymond.

* Bug fix. If Overlap found mate pairs on the same contig with
incorrect orientation, it would generate a misassembled contig.
These misassembled contigs are easily identified in the
xxx-3-overlap.fa file. The two contigs IDs, in the fourth and
fifth column, will be identical.
* New option, --mask-repeat. If two contigs are joined by mate
pairs and are found to overlap by a simple repeat so that the
exact number of the repeat is unknown, join the contigs estimating
the number of the repeat, and mask (lower case) the repeat
sequence. This feature is disabled by default.

* Use gunzip -c rather than zcat for portability.

* New option, --enable-mpich. Use the MPICH2 MPI library.