Accurate isoform discovery with IsoQuant using long reads.
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ABSTRACT:
SUBMITTER: Prjibelski AD
PROVIDER: S-EPMC10344776 | biostudies-literature | 2023 Jul
REPOSITORIES: biostudies-literature
Publications
Accurate isoform discovery with IsoQuant using long reads.
Prjibelski Andrey D AD Mikheenko Alla A Joglekar Anoushka A Smetanin Alexander A Jarroux Julien J Lapidus Alla L AL Tilgner Hagen U HU
Nature biotechnology 20230102 7
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 performa ...[more]
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