This is NOT the official HISAT-genotype Repository. It is only a slight modification of the HISAT-genotype software to allow for easy use of the latest IMGT-HLA reference.
For a guide to building your own indexes, including how to add DRB3, DRB4, and other genes not on the main GRCh38 scaffold, please see here: https://github.com/DrGBL/hisat_genotype_qgp
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/
v1.3.2 - Update to patch critical extract reads error
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.