Trans-ABySS

Analyze ABySS multi-k-assembled shotgun transcriptome data.

Project Description

Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a much smaller set of nonredundant contigs. It contains scripts that map assembled contigs to known transcripts, currently supporting the Blat contig-to-genome aligner. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also identify candidate gene-fusions, single-nucleotide variants, insertions, deletions, and inversions.

The pipeline can be used with other assembly versions, and with other species, once genome and transcript annotation files are available. However, ABySS and Trans-ABySS are general tools that can be used when a reference genome and transcript annotations are unavailable.

The pipeline is written in Python, and typically is used via Perl and shell wrapper scripts.

 

 

 

Current Release
Trans-ABySS 1.4.8

Released Sep 13, 2013

Identifies ITD, PTD, and read-throughs, uses qmake for running pipeline in SGE, and more.
More about this release…

Download file Get Trans-ABySS for Linux
Trans-ABySS 1.4.8 (build 20130916)
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
1.4.8 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
Project Resources

Project owner: Readman Chiu