Accurate isoform discovery with IsoQuant using long reads

Nat Biotechnol. 2023 Jul;41(7):915-918. doi: 10.1038/s41587-022-01565-y. Epub 2023 Jan 2.


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.

MeSH terms

  • Genome
  • High-Throughput Nucleotide Sequencing*
  • Protein Isoforms / genetics
  • RNA*
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA


  • Protein Isoforms
  • RNA