ABySS 1.3.2 (Dec 13, 2011)
Improve distance estimates between contigs, enable scaffolding by default, and remove small shim contigs that don't add useful sequence to the assembly. The default aligner is abyss-map. MergePaths uses a non-greedy algorithm that reduces sequence duplication but may reduce contiguity.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
2011-12-13 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.3.2.
* Enable scaffolding by default.
* Remove small shim contigs.
* Improved distance estimates.
* Reduce sequence duplication.
* Read compressed files on Mac OS X.
abyss-pe:
* Enable scaffolding by default. If the mp parameter is not
specified, use a default value of ${pe} or ${lib}.
* Support using bowtie2 to align reads to contigs by specifying
aligner=bowtie2.
* The default aligner is abyss-map.
* Output the scaffold overlap graph, ${name}-scaffolds.dot.
* Set DYLD_FORCE_FLAT_NAMESPACE to read compressed files on OS X.
ABYSS:
* Can read k-mer count data from a Jellyfish file with extension
.jf for k-mer counts or .jfq for q-mer counts. Jellyfish must be
installed.
* Bug fix. Fix the bug causing the error
bool chomp(std::string&, char): Assertion `s.length() > 1' failed.
abyss-filtergraph:
* New program. Remove small shim contigs that add no useful
sequence to the assembly. Thanks to Tony Raymond (tgr).
PopBubbles:
* New option, -a, --branches. Specify the maximum number of
branches of a bubble that may be popped. Default is 2.
* Use DIALIGN-TX for multiple sequence alignment. Thanks to tgr.
DistanceEst:
* Improved distance estimates.
abyss-joindist:
* Remove this program. Use abyss-todot instead.
MergePaths:
* Use a non-greedy algorithm that reduces sequence duplication but
may reduce contiguity. The greedy algorithm may be used by
specifying the option --greedy.
abyss-fixmate:
* Do not output query names by default.
configure:
* New option, --enable-samseqqual. Enable SAM sequence and quality
fields.
