Accurate isoform discovery with IsoQuant using long reads

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....

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Bibliographic Details
Published in:Nature biotechnology 2023-07, Vol.41 (7), p.915-918
Main Authors: Prjibelski, Andrey D, Mikheenko, Alla, Joglekar, Anoushka, Smetanin, Alexander, Jarroux, Julien, Lapidus, Alla L, Tilgner, Hagen U
Format: Article
Language:English
Subjects:
Annotations
Biotechnology
Brief Communication
Datasets
Gene sequencing
Genes
Genomes
Isoforms
Medicine
Software
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Summary: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.
ISSN:1087-0156
1546-1696
DOI:10.1038/s41587-022-01565-y