Accurate isoform discovery with IsoQuant using long reads

• Published in: Nature biotechnology Vol. 41; no. 7; pp. 915 - 918
• Main Authors: Prjibelski, Andrey D., Mikheenko, Alla, Joglekar, Anoushka, Smetanin, Alexander, Jarroux, Julien, Lapidus, Alla L., Tilgner, Hagen U.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2023; Nature Publishing Group
• Subjects: 631/114/2785; 631/114/794; Agriculture; Annotations; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Brief Communication; Datasets; Gene sequencing; Genes; Genome; Genomes; High-Throughput Nucleotide Sequencing; Isoforms; Life Sciences; Medicine; Protein Isoforms - genetics; RNA; Sequence Analysis, DNA; Sequence Analysis, RNA; Software
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-022-01565-y

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data. IsoQuant predicts novel isoforms from long-read RNA sequencing.