Trans-ABySS 1.0 (Oct 13, 2010)

Pipeline release for the Nature Methods manuscript: "De novo assembly and analysis of RNA-seq data". 2010 Oct 10.

For additional information about this project, please visit the overview page .

Available downloads


For all platforms (126.7 MB)

Release Notes

State Final release
License BCCA (academic use)
User Manual

(pdf file)

Supplementary data (mm9 reads-to-genome alignments) for the mouse transcriptome data SRA012213:
bam file: (7.1G)
bam index file: (4.5M)
BigWig file: (238M)



De novo assembly and analysis of RNA-seq data, Nature Methods. 2010 Oct 10.

Change log

1. This is the official release that accompanies the publication of the manuscript (Robertson et al, Nature Methods, 2010).  The major core analysis modules remain similar to v0.2 but many upgrades have been made in terms of pipeline configuration and file organization.

2. A user manual is provided that details how to run the pipeline.

3. A central wrapper script ("trans-abyss") plus additional helper scripts are available to serve as entry-points in running the pipeline.  They can be found in the "wrappers" sub-folder.

4. Sample data and results are provided in the "sample_data" sub-folder to verify the proper performance of the pipeline.

5. The current pipeline is geared towards finding novel transcript events, finding candidate fusions and estimating gene expression.

6. In addition, the package also includes scripts for finding SNVs and indels (analysis/, as well as finding candidate polyadenylation sites (in "analysis/polyascripts" sub-folder).