IsoQuant is a tool for reference-based analysis of long transcriptomic reads, such as PacBio and ONT. IsoQuant can predict transcript models with and without reference annotation, as well as estimate expression at both gene and transcript level. When reference annotation is provided, 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. 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 github.com/ablab/IsoQuant.