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 the Blat contig-to-genome aligner. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also identify candidate gene-fusions, single-nucleotide variants, insertions, deletions, and inversions.
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 typically is used via Perl and shell wrapper scripts.
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