ABySS 1.2.1 (Jul 12, 2010)
Handle mate pair libraries with reverse-forward orientation as produced by circular, large-fragment libraries. Distance estimates are improved.
For additional information about this project, please visit the overview page .
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Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
2010-07-12 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.2.1.
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
abyss-pe:
* New commands:
se-contigs: Assemble single-end contigs.
pe-contigs: Assemble paired-end contigs (default).
se-sam: Output a gzipped SAM file of the single-end assembly.
se-bam: Ouptut a BAM file of the single-end assembly.
pe-dot: Output a Graphviz dot file of the paired-end assembly.
all: Sam as se-bam pe-contigs pe-dot.
* Options for one particular library may be specified:
lib='lib1 lib2' lib2_s=1000 lib2_n=25
* Input sequence may come from an arbitrary command, which is
useful to assemble a region of an aligned BAM file:
in='<(samtools view genome.bam chr10)'
ABYSS:
* Bug fix. When reading SAM/BAM files, the quality format
incorrectly defaulted to ASCII-64, when it should be ASCII-33.
ABYSS-P:
* May use the Intel MPI library.
ParseAligns:
* Count the number of forward-reverse, reverse-forward and
forward-forward oriented alignments.
DistanceEst:
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
* Remove duplicate mate pairs.
* Print a pretty UTF-8 bar plot of the fragment-size distribution.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.
* Performance improvment.
Overlap:
* Handle cases when more than one gap occurs within the mate pair
fragment size.
SimpleGraph:
* Performance improvment.
MergePaths:
* Handle the case when a circular sequence is assmembled into a
single contig.
abyss-tofastq:
* New program. Convert qseq, export, SAM and BAM files to FASTA or
FASTQ format. The files may be compressed with gz, bz2 or xz and
may be tarred.
