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github.com/DaehwanKimLab/hisat-genotype @v1.3.3

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README

HISAT-genotype

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/

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

Overview

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.

Core symbols most depended-on inside this repo

get_major_nt

called by 14

hisatgenotype_modules/hisatgenotype_assembly_graph.py

get_var_ids

called by 12

hisatgenotype_modules/hisatgenotype_assembly_graph.py

check_files

called by 10

hisatgenotype_modules/hisatgenotype_typing_common.py

check_files

called by 9

etc/hisatgenotype_hla_cyp.py

get_avg_cov

called by 9

hisatgenotype_modules/hisatgenotype_assembly_graph.py

add_count

called by 8

etc/hisatgenotype_hla_cyp.py

write_read

called by 8

hisatgenotype_modules/hisatgenotype_typing_process.py

find_seq_len

called by 7

hisatgenotype_modules/hisatgenotype_typing_process.py

Shape

Function 214

Method 45

Class 3

Languages

Python100%

Modules by API surface

hisatgenotype_modules/hisatgenotype_typing_common.py51 symbols

hisatgenotype_modules/hisatgenotype_assembly_graph.py51 symbols

hisatgenotype_tools/hisatgenotype_extract_cyp_data.py23 symbols

etc/hisatgenotype_hla_cyp.py21 symbols

hisatgenotype_modules/hisatgenotype_args.py19 symbols

hisatgenotype_modules/hisatgenotype_typing_core.py18 symbols

hisatgenotype_modules/hisatgenotype_typing_process.py15 symbols

hisatgenotype_tools/hisatgenotype_extract_RBG.py12 symbols

hisatgenotype_modules/hisatgenotype_validation_check.py11 symbols

hisatgenotype_tools/hisatgenotype_convert_codis.py10 symbols

hisatgenotype_tools/hisatgenotype_legacy.py6 symbols

hisatgenotype_tools/hisatgenotype_locus_samples.py5 symbols

For agents

$ claude mcp add hisat-genotype \
  -- python -m otcore.mcp_server <graph>

⬇ download graph artifact