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Trans-ABySS

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  • trans-abyss

Trans-ABySS


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.


Access mode(s):

Command line on saruman.versailles.inra.fr


Creation date: 05 Jan 2012
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