ABySS 1.3.0 (Sep 09, 2011)
Mate-pair data can be used to scaffold contigs. Specify your mate-pair libraries using the `mp' parameter of abyss-pe.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
Mate-pair data can be used to scaffold contigs. Specify your mate-pair libraries using the `mp' parameter of abyss-pe.
A new short-read mapping program, abyss-map, is included, which uses the Burrows-Wheeler transform and FM-index. To use it, specify the option aligner=map to abyss-pe. This program will produce nearly identical results to KAligner but uses less memory. The output is SAM format.
This release of ABySS requires the Boost C++ Libraries, which can be downloaded here:
http://downloads.sourceforge.net/project/boost/boost/1.47.0/boost_1_47_0.tar.bz2
The bug in MergePaths has been fixed that results in this error message:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.
The bug that would trim quality 41 bases from the ends of reads has been fixed.
CASAVA-formatted FASTQ files are supported.
Change log
2011-09-09 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.3.0.
* Use mate-pair libraries to scaffold contigs.
* Support CASAVA-formatted FASTQ files.
* Bug fix. Do not trim quality 41 bases from the ends of reads.
* Boost C++ Libraries are required to compile ABySS.
abyss-pe:
* New parameter, mp, to specify the mate-pair libraries to be used
for scaffolding.
* Increase the default value for s from 100 to 200.
* Set the default value for n to 10.
* Integrate with PBS.
abyss-scaffold:
* New program. Scaffold using mate-pair libraries.
DistanceEst:
* Ignore multimapped alignments with a mapping quality of zero.
* New option, -q, --min-mapq. Ignore alignments with mapping
quality less than this threshold. Default is 1.
* Do not use OpenMP 3.0.
PopBubbles:
* Scaffold over complex bubbles with the option --scaffold.
Disabled by default.
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.
* New option, --no-greedy. Use a non-greedy algorithm that reduces
sequence duplication but reduces contiguity. Disabled by default.
KAligner:
* Performance improvements. Thanks to Tony Raymond (tgr).
* The output is printed in the same order as the input when
multithreaded. (tgr)
abyss-map:
* New program. Use the BWT and FM-index to find the longest common
substring. To use it, specify the option aligner=map to abyss-pe.
abyss-index:
* New program. Build a FM-index of a FASTA file.
abyss-bowtie:
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-bwa:
* Use bwa index -a bwtsw by default.
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-fac:
* Report N80, N50 and N20. Do not report median and mean.
* Increase the default minimum contig size threshold, option -t,
from 100 to 200.
abyss-fixmate:
* Set the mapping quality of both alignments to the minimum
mapping quality of the pair of alignments.
abyss-tofastq:
* New option, -i, --interleave. Interleave the files.
configure:
* New option, --with-boost. Specify the path for Boost.
* New option, --disable-popcnt. Do not use the popcnt instruction.
