ABySS 1.3.3 (Mar 13, 2012)
Specify the minimum alignment length when aligning the reads to the contigs with the parameter l. Improve the scaffolding algorithm that identifies repeats. Improve the documentation.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
2012-03-13 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.3.3.
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs.
* Improve the scaffolding algorithm that identifies repeats.
* Improve the documentation.
abyss-pe:
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs. This option may be specified
per library. The default value is k.
* New parameter, S. Specify the minimum contig size required for
building scaffolds.
* New parameter, N. Specify the minimum number of pairs required
for building scaffolds.
* Integrate with Load Sharing Facility (LSF).
* Calculate the assembly contiguity statistics.
KAligner, abyss-map:
* Rename the minimum alignment length option -k to -l.
DistanceEst:
* Dual licensed under the GPL and BCCA-Academic licenses.
* New options, --fr and --rf. Specify the orientation of the
library. The default behaviour is to detect the orientation.
* New options, --mind and --maxd. Specify the minimum and maximum
distances for the maximum likelihood estimator.
* New option, -l, --min-align. Specify the minimum alignment
length of the aligner, which can improve distance estimates.
* Increase the default minimum mapping quality, -q, to 10, was 1.
MergePaths:
* Bug fix. Fix the bug causing the error:
Assertion `count(it2+1, path2.end(), pivot) == 0' failed.
PathConsensus:
* Bug fix. Fix the bug causing the error:
Assertion `fstSol.size() == sndSol.size()' failed.
MergeContigs:
* Calculate the assembly contiguity statistics.
abyss-scaffold:
* Improve the algorithm that identifies repeats.
* Remove simple cycles from the scaffold graph.
* Calculate the assembly contiguity statistics.
* The option -s may specify a range, such as -s200-10000,
to find the value of s that maximizes the scaffold N50.
abyss-fac:
* New option, -m, --mmd. Output MultiMarkdown format.
abyss-index:
* New option, -a, --alphabet. Specify the alphabet.
* New option, --bwt. Output the Burrows-Wheeler transform.
abyss-samtoafg:
* New script. Convert a SAM file to an AMOS AFG file.
README, README.html, abyss-pe.1:
* Improve the documentation.
