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:
- 09/01/2020: HISAT-genotype 1.3.2 release
- Patched critical error during read extractin that prevented proper use of the reference
- Fixed bug in assembly code
- Added devel folder for CI and as a test bed
- General bug fixes
- 08/27/2020: HISAT-genotype 1.3.1 release
- setup.sh script now works properly and has been given option to predownload required indicies
- parse-results script has been added to hisatgenotype_toolkit and can be used to parse the report files into something more managable in downstream applications and can limit the reported allele digits/files
- –assembly option now will also output a fasta file with the constructed allele sequences
- Added -z/–index_dir option to hisatgenotype that will tell hisatgenotype where to look for/download indicies
- General bug fixes and improvements to stability
- 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
- 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.
hisatgenotypeandhisatgenotype_toolkitruns 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
- Wrapper has been added to HISAT-genotype.
- 02/01/2018: HISAT-genotype 1.0.1-beta release
- HLA assembly results are reported in the PDF format, instead of the HTML format.
- 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.