ABySS 1.3.5 (Mar 05, 2013)

ABySS

This release introduces new tools to merge overlapping read pairs, layout and merge contigs with perfect sequence overlap, and calculate contig contiguity and correctness metrics. Also, it includes updates to the existing documentation, bug fixes, and attempts to fill scaffold gaps with a consensus of all paths between contigs.

For additional information about this project, please visit the overview page .

Available downloads

Source

For all platforms (635.8 KB)

Test input data (paired end reads)

For all platforms (1.4 MB)

Release Notes

State Final release
License BCCA (academic use)

2013-03-04 Anthony Raymond <traymond@bcgsc.ca>

* Release version 1.3.5
* Standardized --help message format.
* Improve documentation.
* Merge overlapping read pairs.
* Layout and merge contigs using sequence overlap graph.
* Attempt to fill scaffold gap with consensus of all paths between
contigs.

abyss-pe:
* Attempt to fill scaffold gap with consensus of all paths between
contigs.

AdjList:
* Increase the default value of m from 30 to 50.

abyss-overlap:
* Increase the default value of m from 30 to 50.
* New options, --tred and --no-tred. Remove transitive edges.
Default --tred.

abyss-mergepairs:
* New program. Merges overlapping read pairs.

ABYSS-P:
* Bug fix. Exit when there is a problem reading a file.
* Don't store sequences in the rank 0 process when using at least
1000 cores. Improves memory distribution with large number of
cores.

abyss-fac:
* Increase the default value of t from 200 to 500.

DistanceEst:
* Bug fix. Exit with success if there is only one contig. Fixes
this error:
DistanceEst: DistanceEst.cpp:534: int main(int, char**): Assertion `in' failed.
* Bug fix. Fix the bug causing this error:
DistanceEst: error: The observed fragment of size 128 bp is shorter than 2*l (l=71). Decrease l to 64.
* Bug fix. Correctly estimate distance using MLE when l=0.

abyss-layout:
* New program. Layout contigs using the sequence overlap graph.

abyss-map:
* Return helpful error when query ID starts with '@`
* New options, --chastity and --no-chastity. Ignore chastity
failed reads. Default --no-chastity.

abyss-samtobreak:
* New script. Calculate contig and scaffold contiguity and
correctness metrics.

abyss-fixmate:
* New option, l. Minimum alignment length. Set unmapped flag if
the CIGAR match length is too small.
* Print all alignments when the histogram output file not given.
* Print SAM header to the same file when given.