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This is the official HISAT-genotype Repository.

Please see the official website for HISATgenotype:

This directory no longer contains HISAT2. Please see the link below if you are looking for the newest HISAT2 release

Current Release Version

v1.3.2 - Update to patch critical extract reads error

Previous Releases

v1.3.1 - Update database locations and handling, and general stability fixes - BROKEN

v1.3.0 - Python 3 version


HISAT-genotype is a next-generation genomic analysis software platform capable of assembling and genotyping human genes and genomic regions. Thie software leverages HISAT2s graph FM index and graph alignemnt algorithm to align reads to a specially constructed graph genome. An Expectation-Maximization (EM) algorithm finds the maximum likelihood estimates for each gene allele and a guided de Bruijn graph is used to construct the allele sequences.