Trans-ABySS

de novo assembly of RNA-Seq data using ABySS

Project Description

The current version of the Trans-ABySS package comes with 3 main applications:

1. transabyss - assemble RNAseq data

2. transabyss-merge - merge multiple assemblies from (1)

3. transabyss-analyze - analyze assemblies, either from (1) or (2), for structural variants and splice variants. Requires reference genome and annotations.

Current Release
Trans-ABySS 1.5.1

Released Jul 22, 2014

Support strand-specific RNAseq data. Major improvement in assembly quality; both rare and common transcripts can be assembled well with "small" k-mer sizes (ie. 25~32).
More about this release…

Download file Get Trans-ABySS for Linux
transabyss-1.5.1.zip
If you are using Plone 3.2 or higher, you probably want to install this product with buildout. See our tutorial on installing add-on products with buildout for more information.

All Releases

Version Released Description Compatibility Licenses Status
1.5.1 Jul 22, 2014 Support strand-specific RNAseq data. Major improvement in assembly quality; both rare and common transcripts can be assembled well with "small" k-mer sizes (ie. 25~32). More about this release… BCCA (academic use) final
1.4.8 Sep 13, 2013 Identifies ITD, PTD, and read-throughs, uses qmake for running pipeline in SGE, and more. More about this release… BCCA (academic use) final
1.4.4 Oct 09, 2012 Supports both transcriptome and genome assemblies. A more robust pipeline and improvement to the 3 analysis suites (fusions, indels, and splicing). More about this release… BCCA (academic use) final
1.3.5 Sep 13, 2012 Lowered contig size filtering cutoff from 2k-1 to 2k-10; various improvement to fusions and indel code (see ChangeLog) More about this release… BCCA (academic use) final
1.3.2 Feb 29, 2012 Compatibility with ABySS 1.3.2; Streamlining of pipeline and configuration files; Analysis code improvement More about this release… BCCA (academic use) final
1.2.0 Jan 07, 2011 Bug fixes and performance improved for chimeric transcript codes; also fixed assembly.py to handle output from different ABySS versions More about this release… BCCA (academic use) final
1.1.0 Nov 22, 2010 Added new code for finding putative chimeric transcripts, and adjusted stage 1 filtering to reduce the number of small contigs. More about this release… BCCA (academic use) final
1.0.1 Nov 03, 2010 This release includes updated filtering prior to assembly merging (assembly.py), an updated model_matcher.py, numerous other feature improvements and bug fixes. More about this release… BCCA (academic use) final
1.0 Oct 13, 2010 Pipeline release for the Nature Methods manuscript: "De novo assembly and analysis of RNA-seq data". 2010 Oct 10. More about this release… BCCA (academic use) final
0.2 May 26, 2010 Addition of scripts for novel poly-adenylation site detection and novel anomalous contig detection. More about this release… AFL final
0.1 Apr 14, 2010 Initial Trans-ABySS release More about this release… AFL final