Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser

Abstract BackgroundLong-read RNA sequencing, such as Pacific Biosciences’ Iso-Seq method, enables generation of sequencing reads that are 10 kilobases or even longer. These reads are ideal for discovering splice junctions and resolving full-length gene transcripts without time-consuming and error-prone techniques such as transcript assembly and junction inference. ResultsIso-Seq Browser is a Web-based visual analytics tool for long-read RNA sequencing data produced by Pacific Biosciences’ isoform sequencing (Iso-Seq) techniques. Key features of the Iso-Seq Browser are: 1) an exon-only web-based interface with zooming and exon highlighting for exploring reference gene transcripts and novel gene isoforms, 2) automated grouping of transcripts and isoforms by similarity, 3) many customization features for data exploration and creating publication ready figures, and 4) exporting selected isoforms into fasta files for further analysis. Iso-Seq Browser is written in Python using several scientific libraries. The application and analyses described in this paper are freely available to both academic and commercial users at https://github.com/goeckslab/isoseq-browser ConclusionsIso-Seq Browser enables interactive genome-wide visual analysis of long RNA sequence reads. Through visualization, highlighting, clustering, and filtering of gene isoforms, ISB makes it simple to identify novel isoforms and novel isoform features such as exons, introns and untranslated regions.