IsoQuant

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. If reads are grouped (e.g. according to a cell type), counts are reported according to the provided grouping.

The latest IsoQuant version can be downloaded from github.com/ablab/IsoQuant/releases/latest.

Full IsoQuant documentation is available at ablab.github.io/IsoQuant.