ABySS 1.5.0 (May 01, 2014)
In this release we have added full strand specific RNA-Seq support such that output contigs are correctly oriented with respect to the original transcripts sequenced. Also, there are new parameters to abyss-pe, xtip and Q, that are used to improve assembly in high coverage regions like highly expressed transcripts. Setting xtip=1 will more aggressively remove certain tips. The 'Q' parameter will prevent low quality bases from being used in the assembly. The version has been bumped to 1.5.0 to signify compatibility with Trans-ABySS 1.5.0.
For additional information about this project, please visit the overview page .
Available downloads
Change log
2014-01-15 Anthony Raymond <traymond@bcgsc.ca>
* Release version 1.5.0
* Assemble strand-specific RNA-Seq libraries into strand-specific
contigs.
* New parameters, Q and xtip. Improves assembly in high-coverage
regions by removing recurrent read errors.
* Portability fixes for Fujitsu C Compiler.
abyss-pe:
* New parameter, `Q`, to mask low quality bases to N.
* New parameter, `xtip=1`, to remove 2-in 0-out tips.
* New parameter, `ss=1`, to perform strand-specific assembly
using ssRNA-Seq libraries.
* New command, `scaftigs`. Breaks scaffold sequences at 'N's and
produce a scaftigs.fa file.
* Include long-scaffs.fa in FAC statistics if `long` parameter
used.
abyss-fixmate:
* Performance improvement for GCC-4.6 and older.
DistanceEst:
* Report an estimation of duplicate fragments from read pairs
mapping to different contigs.
abyss-fixmate:
* Report number of fragments removed as noise and outliers.
ABYSS/ABYSS-P:
* New option, --SS, to support strand-specific assembly.
abyss-layout:
* New option, --SS, to support strand-specific assembly.
abyss-map:
* New option, --SS, to support strand-specific assembly.
abyss-overlap:
* New option, --SS, to support strand-specific assembly.
abyss-PathOverlap:
* New option, --SS, to support strand-specific assembly.
abyss-scaffold:
* New option, --SS, to support strand-specific assembly.
* Don't prune xtips when scaffolding.
AdjList:
* New option, --SS, to support strand-specific assembly.
Overlap:
* New option, --SS, to support strand-specific assembly.
PopBubbles:
* New option, --SS, to support strand-specific assembly.
