Releases

Existing and upcoming releases for this project.

« Back to project page

Experimental Releases

Stable Releases

ABySS 1.2.2 (Aug 25, 2010)
Merge contigs after popping bubbles. Handle multi-line FASTA sequences. Report the amount of memory used.
Read more…
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.
Read more…
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.
Read more…
ABySS 1.1.2 (Feb 15, 2010)
Pop bubbles resulting from indels. Read tar files. Fix performance issues in ParseAligns by syncing KAligner threads periodically.
Read more…
ABySS 1.1.1 (Jan 19, 2010)
Pop complex bubbles either completely or not at all. Choose better (typically lower) default values for the parameters e and c.
Read more…
ABySS 1.1.0 (Dec 21, 2009)
ABySS will expand tandem repeats when it is possible to determine the exact number of the repeat. The paired-end path-finding algorithm, SimpleGraph, is multithreaded. Fixed a bug in MergePaths that could misassemble repeats larger than the paired-end fragment size. The output format of AdjList, DistanceEst and SimpleGraph has changed.
Read more…
ABySS 1.0.16 (Nov 13, 2009)
Improve the performance and memory usage of KAligner and AdjList, particularly for very large data sets.
Read more…
ABySS 1.0.15 (Oct 19, 2009)
New parameters, e and E, to set the coverage threshold of the erosion algorithm. Values for the parameters e and the coverage threshold, c, will be chosen automatically if they're not specified. The read length is now an optional parameter. Two important bug fixes, see below.
Read more…
ABySS 1.0.14 (Sep 08, 2009)
Assemble multiple libraries of different fragment sizes.
Read more…
ABySS 1.0.13 (Aug 26, 2009)
Read files compressed with gzip (.gz) or bzip2 (.bz2).
Read more…
ABySS 1.0.12 (Aug 19, 2009)
Both ABYSS and KAligner are run only once per assembly, which speeds up the paired-end assembly stage by nearly a factor of two. The k-mer coverage information is correct in every contig file. A tool is included to convert colour-space contigs to nucleotide contigs. Discard reads that fail the chastity filter.
Read more…
ABySS 1.0.11 (Jul 21, 2009)
Assemble colour-space reads. Read files in qseq format. KAligner is multithreaded. Integrate with Sun Grid Engine (SGE). Prevent misassemblies mediated by tandem segmental duplications.
Read more…
ABySS 1.0.10 (Jun 18, 2009)
ParseAligns is improved to handle any number of reads as long as mate pairs are found interleaved in the same file. Merge overlapping paired-end contigs that were previously being missed in some situations. Number paired-end contigs so that their IDs do not overlap with the single-end contigs.
Read more…
ABySS 1.0.9 (May 15, 2009)
Significantly reduce the memory usage of KAligner and ParseAligns. abyss-pe can read multiple input files and read FASTA or FASTQ files.
Read more…
ABySS 1.0.8 (Apr 02, 2009)
Fix the bug causing the error Assertion `marked == split' failed.
Read more…
ABySS 1.0.7 (Mar 31, 2009)
The parallel MPI assembler is now deterministic; it will produce the same result every time.
Read more…
ABySS 1.0.6 (Mar 25, 2009)
Fix a race condition in the erosion algorithm.
Read more…
ABySS 1.0.5 (Mar 11, 2009)
Portability fixes.
Read more…
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.
Read more…
ABySS 1.0.3 (Feb 05, 2009)
Tidy up the ends of blunt contigs. Merge blunt contigs that are connected by pairs and overlap.
Read more…
ABySS 1.0.2 (Nov 21, 2008)
Include a parallel binary compiled for OpenMPI.
Read more…
ABySS 1.0 (Aug 07, 2008)
Initial version of abyss.
Read more…