IsoQuant is a tool for reference-based analysis of long error-prone transcriptomic reads. IsoQuant assigns reads to annotated isoforms based on their intron and exon structure, and further performs gene and isoform quantification. For high-error-rate data, the algorithm uses inexact intron and exon matching, which accurately resolves various error-rate induced alignment artifacts, such as skipped short exons or shifted splice sites. IsoQuant also generates known and novel transcript models based on long reads and gene annotation. Additionally, it can group counts of various genomic features, which can be useful for analyzing single-cell and spatial transcriptomic data.

IsoQuant is an open-source software implemented in Python and is available at


  1. Andrey D Prjibelski , Alla Mikheenko , Anoushka Joglekar, Dmitry Meleshko , Alla L Lapidus , Hagen Tilgner IsoQuant: isoform analysis and quantification with long error-prone transcriptomic reads (talk), 2020