TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts

MOTIVATION: Long-read, single-molecule sequencing platforms hold great potential for isoform discovery and characterization of multi-exon transcripts. However, their high error rates are an obstacle to distinguishing novel transcript isoforms from sequencing artifacts. Therefore, we developed the package TranscriptClean to correct mismatches, microindels and noncanonical splice junctions in mapped transcripts using the reference genome while preserving known variants. RESULTS: Our method corrects nearly all mismatches and indels present in a publically available human PacBio Iso-seq dataset, and rescues 39% of noncanonical splice junctions. AVAILABILITY AND IMPLEMENTATION: All Python and R scripts used in this paper are available at https://github.com/dewyman/TranscriptClean.