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 Blat and Exonerate contig-to-genome aligners. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also estimate gene expression levels, identify candidate polyadenylation sites, and identify candidate gene-fusion events.

The work reported in the publication involved mouse and human data, and the download includes transcript annotation files for human (hg18) and mouse (mm9). 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 Perl, and typically is used via Perl wrapper scripts.

 

The following are annotation files for hg18 and mm9 genomes as used by trans-ABySS pipeline:

download hg18 annotation files

download mm9 annotation files