This is the official HISAT-genotype Repository.
Please see the official website for HISATgenotype: https://daehwankimlab.github.io/hisat-genotype/
This directory no longer contains HISAT2. Please see the link below if you are looking for the newest HISAT2 release https://daehwankimlab.github.io/hisat2/
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.