📚 Tools and databases for analyzing HLA and VDJ genes.

xHLA: Fast and accurate HLA typing from short read sequence data

Precision HLA typing from next-generation sequencing data

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

Kourami: Graph-guided assembly for HLA alleles

An HLA star-calling tool for PacBio HiFi data types

Clinical Whole Genome and Exome Sequencing Pipeline

HLA typing for Sanger Based Test

R package specialized in HLA typing clustering and visualization based on specific similarity metrics

A script to run HLA typing tools from next generation sequencing data

A Nextflow workflow for HLA typing using HLA-HD

RNA2HLA is a QC tool performing study-wide HLA typing for RNA-seq data (paired on single-end) and thereby identifying the samples from the common source.

hla-typing by optitype & polysolver , detect loh by lohhla.

Python package for doing fast and accurate sequence annotation

Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS and amplicon data. It supports PacBio and Nanopore data.

Data portal and API for Center for Viral Systems Biology (CViSB) data

HLAXPress performs estimation of allele-specific expression levels for HLA genes using UMIs.

FHIR Implementation Guide for HLA reporting

HLA typing pipelines in nextflow