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

  1. transabyss: assemble RNAseq data
  2. transabyss-merge: merge multiple assemblies from (1)

Current Release

GitHub release page for Trans-ABySS

All Releases

Version  Released  Description  Licenses  Status 
2.0.1 Feb 19, 2018 Switch to GPL3 license, support for Python 3 GPLv3 for non-commercial usage final
2.0.0 Feb 05, 2018 Supports ABySS 2.0 BCCA (academic use) final
1.5.5 Aug 02, 2016 Set default shortest contig length to 100 bp. Skip blat alignments during assembly BCCA (academic use) final
1.5.4 May 09, 2016 Removed transabyss-analyze and its associated modules. We recommend using PAVFinder for structural variant detection BCCA (academic use) final
1.5.3 May 22, 2015 A few bug-fixes; no major changes to assembly algorithms BCCA (academic use) final
1.5.2 Nov 14, 2014 Simplify the installation of required softwares. Less temporary disk space usage in assembly. New options, bugfixes, and improvements BCCA (academic use) final
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) 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 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) 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) 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 BCCA (academic use) final
1.2.0 Jan 07, 2011 Bug fixes and performance improved for chimeric transcript codes; also fixed to handle output from different ABySS versions 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 BCCA (academic use) final
1.0.1 Nov 03, 2010 This release includes updated filtering prior to assembly merging (, an updated, numerous other feature improvements and bug fixes 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 BCCA (academic use) final
0.2 May 26, 2010 Addition of scripts for novel poly-adenylation site detection and novel anomalous contig detection AFL final
0.1 Apr 14, 2010 Initial Trans-ABySS release AFL final
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