Accurate isoform discovery with IsoQuant using long reads
Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux, Alla L Lapidus, Hagen Tilgner · Nature Biotechnology · 2023
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.