Barnacle

A pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly. It identifies sequences with a variety of anomalous alignment topologies, predicts partial tandem duplications (PTDs), internal tandem duplications (ITDS), and fusions from these sequences, and measures the coverage of the inferred chimeric transcripts relative to corresponding wild-type transcripts.

Project Description

The Barnacle pipeline is composed of five stages:
Stage 1) examine contig-to-genome alignments and identify anomalous or non-reference (candidate) contigs that have a variety of alignment topologies,
Stage 2) examine transcriptome read alignments to assembled contig sequences and calculate read support for these candidate contigs,
Stage 3) apply user-specified filters to the candidate contigs and retain only sufficiently confident candidates,
Stage 4) identify chimeric transcripts of particular types (PTDs, ITDs, and fusions) from the filtered candidates,
Stage 5) compare the coverage of the predicted chimeric transcripts to their corresponding wild-type transcripts.