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Software Release ABySS 1.2.3
by Shaun Jackman published Sep 08, 2010
Fix two bugs that caused the error messages: Assertion `m_comm.receiveEmpty()' failed. and error: unexpected ID
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.2.4
by Shaun Jackman published Oct 14, 2010
Replace gaps of Ns that span a region of ambiguous sequence with a consensus sequence of the possible sequences that fill the gap. The consensus sequence uses IUPAC-IUB ambiguity codes.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.2.5
by Shaun Jackman published Nov 15, 2010 last modified Nov 15, 2010 03:52 PM
Fix a colour-space-specific bug and a bug causing the error Assertion `fstSol.size() == 1' failed.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.2.6
by Shaun Jackman published Feb 07, 2011 last modified Feb 07, 2011 04:44 PM
Sequence variants are popped if the two variants are at least 90% similar. Contigs that overlap by fewer than k-1 bp are found and may be merged.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.2.7
by Shaun Jackman published Apr 15, 2011 last modified Apr 15, 2011 05:45 PM
Support using bwa or bowtie to align reads to contigs. New parameter, d, to specify the acceptable error of a distance estimate.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.0
by Shaun Jackman published Sep 09, 2011 last modified Sep 09, 2011 05:25 PM
Mate-pair data can be used to scaffold contigs. Specify your mate-pair libraries using the `mp' parameter of abyss-pe.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.1
by Shaun Jackman published Oct 24, 2011 last modified Oct 24, 2011 01:29 PM
Fix a bug in KAligner and fix a compiler error for Mac OS X.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.2
by Shaun Jackman published Dec 13, 2011 last modified Dec 13, 2011 04:43 PM
Improve distance estimates between contigs, enable scaffolding by default, and remove small shim contigs that don't add useful sequence to the assembly. The default aligner is abyss-map. MergePaths uses a non-greedy algorithm that reduces sequence duplication but may reduce contiguity.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.3
by Shaun Jackman published Mar 13, 2012 last modified May 30, 2012 04:07 PM
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.
Located in Platforms / / ABySS / Releases
Software Release ABySS 1.3.4
by Shaun Jackman published May 30, 2012 last modified May 30, 2012 04:07 PM
This release eliminates two sources of misassemblies, one in the path extension logic of SimpleGraph. Two, the default value of m, which is the minimum overlap required between two contigs to merge them, is increased from 30 to 50. This release also fixes various portability issues. A new script, abyss-fatoagp, is included to create an AGP file for GenBank submission.
Located in Platforms / / ABySS / Releases