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TAPIS / Transcriptome Analysis Pipeline from Isoform Sequencing
Allows investigation of Iso-Seq data. TAPIS aims to correct errors, align reads to the reference genome, find all splice isoforms and alternative splicing (AS) events generated from a gene and 3’ heterogeneities because of alternative polyadenylation (APA) sites. It represents an iterative process that alternates read mapping and error correction on the basis of the reference genome. This tool is able to cooperate a two-stage error-correction in the neighbourhood of splice junctions.
IsoCon
Allows determination of the full-length transcripts of highly similar multicopy gene families. IsoCon enables error-correction and removes redundancy of PacBio circular consensus sequence (CCS) reads generated from targeted sequencing with the Iso-Seq protocol. The software consists of two main steps: (i) an iterative clustering algorithm to error-correct the reads and identify candidate transcripts, and (ii) iterative removal of statistically insignificant candidates. It can capture transcripts that differ by only one nucleotide in sequence and by three orders of magnitude in abundance.
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