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.
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News and Releases:

  • 05/20/2020: HISAT-genotype 1.3.0 release
    • Python 3.7 is now the base python HISATgenotype is built upon
    • Core scripts have been further consolidated and collapsed with redundant code being removed
    • hisatgenotype_script folder has been renamed etc and now contains mostly accessory scripts
    • debug argument is now fully random when testing allele combinations
    • Each python module now has a flag for degugging and running sanity checks
    • Results are now sorted alphabetically
    • Added tool to concolidate and simplify results from HISAT-genotype
    • Added Setup script to aid HISAT-genotype initial set-up
    • HISAT-genotype now uses the latest version of HISAT2 and tracks versions
    • Results are output to a result file by default
    • Reworked Github repo structure for easy access to different version
  • 01/23/2020: HISAT-genotype 1.1.3 release
    • Incremental change to address bugs with using -U option
  • 07/11/2019: HISAT-genotype 1.1.2-beta release
    • Wrapper has been added to HISAT-genotype. hisatgenotype and hisatgenotype_toolkit runs the entirety of HISAT-genotype
    • Argument names for scripts have been made more consistent
    • HISAT-genotype code has been consolidated into modules. All core functionality is now in modules
    • Scripts for HISAT-genotype have been consolidated into single directory and are runnable through hisatgenotype_toolkit
    • Changes made to debug mode to prevent overwritting of debug results through each iteration
    • Advanced arguments are hidden by default in hisatgentoype

  • 02/01/2018: HISAT-genotype 1.0.1-beta release
    • HLA assembly results are reported in the PDF format, instead of the HTML format.

  • 06/08/2017: HISAT-genotype 1.0.0-beta release (first release)
    • HISAT-genotype currently supports HLA typing, the discovery of novel HLA alleles, DNA fingerprinting analysis, and CYP2D6 typing.
    • The platform is currently designed for processing whole genome sequencing reads produced by Illumina platforms (e.g. 100 to 300 bps) and works great with paired-end reads and at least 20x coverage.
    • We plan to create consortia to work together in enabling the platform to analyze the whole human genome with its >20,000 genes.

  • 06/08/2017: The HISAT-genotype source code is available in a public GitHub repository.

HISAT2, github
HISAT-genotype FTP