ABySS 1.0.4 (Mar 09, 2009)


Remove the need to specify the parameters -e,--erode and -b,--bubbles. Use less disk space by using pipes to avoid intermediate files. Many improvements to the paired-end algorithm.

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

Available downloads


For all platforms (212 kB)

Release Notes

State Final release
License BCCA (academic use)

2009-03-04 Shaun Jackman <sjackman@bcgsc.ca>

* Release version 1.0.4.

* Remove the need to specify a -e,--erode parameter by improving
the erosion algorithm to complete in a single pass.
* Removet the default limit on the maximum number of bubble
popping rounds. A limit may be specified using -b,--bubbles.
* Generate a warning if an input file is empty, but do not die.
* When using a Google sparsehash, allocate room for 100 million
* Increase the maximum FASTA line length from 64 kB to 256 kB.
* Require only one of either -l,--read-length or -t,--trim-length
to be specified.
* Allow read pairs to be named `_forward' and `_reverse'.
* Ensure that exactly k-1 bases of context is given on each side
of the bubble sequence. Previously, one side would have k bases of
context, and the other side would have k-1 bases.
* Add command line options to each of the paired-end programs.

* Use Open MPI as the default MPI library.
* Do not link against the Open MPI C++ library.

* Use pipes where possible to avoid intermediate files.
* The semantics of the n argument have changed. See DistanceEst
-n,--npairs below.

* If more than one path is found but only one meets all of the
constraints, use it.
* Allow for some constant error in distance estimates that does
not decrease with the number of samples. The expected fragment
size seems to vary with genomic coordinate to a certain degree.
So, the distribution of fragment size spanning two given contigs
may differ from the empirical distribution by a roughly constant

* The semantics of the -n,--npairs option has changed.
Require at least NPAIRS pairs between contigs (>= NPAIRS).
Previously, required strictly more than NPAIRS pairs between
contigs (> NPAIRS).
* Give the estimated error to a single decimal place.
* When counting the number of pairs that join two contigs, only
count pairs that fit the empirical distribution.
* When deciding whether the pairs joining two contigs are
inconsistent in sense, require NPAIRS read pairs joining two
contigs in each sense before considering the pair data to be

* Measure fragments in total size, not alignment distance.
* Allow a read that spans two contigs to be used in distance
* Add the -h,--hist option to produce a histogram.
* Bug fix. When measuring the empirical fragment size, ensure that
the sense of the alignments is correct. Output a negative fragment
size if the reverse read aligns ahead of the forward read.
* Bug fix. Miscalculated the fragment size estimate between two
contigs if they did not have the same sense and one contig
required flipping. It was possible to see one distance estimate
from contig A to contig B and a differing estimate from contig B
to contig A. Typically, the distance estimate would be off by