The current version of the Trans-ABySS package comes with the following applications:
- transabyss: assemble RNAseq data
- 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 assembly.py 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 (assembly.py), an updated model_matcher.py, 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 |