ABySS 1.2.0 (May 26, 2010)
Scaffold over gaps in coverage and unresolved repeats. Read sequence from SAM and BAM files. Set q=3 by default. Set E=0 when coverage is low (<2). Generate a Graphviz dot file of the paired-end assembly.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
2010-05-25 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.2.0.
* Scaffold over gaps in coverage and unresolved repetitive
sequence using Ns.
* Read sequence from SAM and BAM files.
abyss-pe:
* Set q=3 by default. Trim bases from the ends of reads whose
quality is less than 3.
* Do not store the .pair.gz file.
* Generate a BAM file of the mate pairs that align to
different contigs of the single-end assembly. Disabled by default.
* Output a Graphviz dot file of the paired-end assembly.
Disabled by default.
* Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa.
* Store the indel bubbles in ${name}-indel.fa.
* Bug fix for mawk.
ABYSS:
* Set -E0 when coverage is low (<2).
ABYSS-P:
* Remove the temporary files contigs-*.fa and snp-*.fa.
PopBubbles:
* Output in Graphviz dot format using --dot.
KAligner:
* Do not ignore sequences (reads or contigs) containing N.
* Output SAM headers (but not SAM alignments).
ParseAligns:
* Output in SAM format.
DistanceEst:
* Input in SAM format.
* Output in Graphviz dot format using --dot.
Overlap:
* Scaffold over gaps in coverage. Scaffolding can be disabled
using the option --no-scaffold.
* Merge contigs that overlap at simple repeats. These merges can
be prevented using the option --no-merge-repeat.
SimpleGraph:
* Scaffold over repeats. Scaffolding can be disabled using the
option --no-scaffold.
MergePaths:
* Merge paths containing ambiguous sequence.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.
MergeContigs:
* Merge paths and contigs containing ambiguous sequence.
PathOverlap:
* Output in Graphviz dot format using --dot.
Consensus:
* Output the pileup in samtools format.
