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.

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

Available downloads

Source

For all platforms (232 kB)

Release Notes

2009-08-18 Shaun Jackman <sjackman@bcgsc.ca>

* Release version 1.0.12.

abyss-pe:
* Both ABYSS and KAligner are run only once per assembly, which
speeds up the paired-end assembly by nearly a factor of two.
* The k-mer coverage information is correct in every contig file.
* A new parameter, cs, converts colour-space contigs to nucleotide
contigs using Consensus.
* A new parameter, ABYSS_OPTIONS, may be used to disable chastity
filtering by specifying ABYSS_OPTIONS=--no-chastity.

ABYSS:
* Read files in export format, which is similar to qseq format.
* Discard reads that failed the chastity filter. Use the
--no-chastity option to retain these unchaste reads. Chastity
filtering affects only qseq- and export formatted-files.
* Remove low-coverage contigs within ABYSS rather than filtering
using awk and reassembling.
* Support big-endian architecture machines.

KAligner:
* A new option, -m or --multimap, specifies that a duplicate k-mer
may be seen in the target sequence. By default, every k-mer in the
target sequence must be unique.
* A new option, --seq, prints the read sequence of each alignment.

Overlap:
* A new option, --scaffold, fills the gap between two blunt
contigs with Ns. This feature is disabled by default.

Consensus:
* Call the consensus sequence for each contig based on the
alignment of reads to contigs.
* Convert colour-space contigs to nucleotide contigs.
* Written by Tony Raymond.