TABLE 1.
Tools for HLA analyses.
| HLA application name | Description | URL |
|---|---|---|
| Alphlard-nt (Hayashi et al., 2019) | Identification of somatic mutations in HLA molecules from whole-genome and exome data using Bayesian algorithms | — |
| BIGDAWG (Pappas et al., 2016) | Open-source R package for the case-control analysis of highly polymorphic data at the allele, haplotype and amino-acid level | https://CRAN.R-project.org/package=BIGDAWG |
| Easy-HLA (Geffard et al., 2020) | Website with HLA alleles haplotyping, upgrading and inference from HLA genotypes, prediction of HLA-C expression | http://hla.univ-nantes.fr/ |
| HATK (Choi et al., 2021) | Open-source Python pipeline for HLA association studies, including tools for HLA data formatting | https://github.com/WansonChoi/HATK |
| HLA-check (Jeanmougin et al., 2017) | Perl tool evaluating the probability of accurate HLA genotype imputation by comparing it to SNP imputation in the exonic region of HLA. | https://github.com/mclegrand/HLA-check/ |
| HLA-EMMA (Kramer et al., 2020) | Donor/recipient compatibility assessment based on solvent-accesible amino acids, based on intralocus comparisons | http://www.HLA-EMMA.com |
| HLAfix | Open-source R pipeline for HLA association studies. Performing SNP quality control steps, stratification, HLA imputation and representation of the results | https://univ-nantes.io/Nico_V/hlafix |
| HLAHapV (Osoegawa et al., 2016) | A Java-based HLA Haplotype Validator for quality assessments of HLA typing | https://github.com/nmdp-bioinformatics/ImmunogeneticDataTools |
| HLA-NET (Nunes et al., 2014) | Set of tools to manipulate HLA data, infer haplotypes, convert files format, and information about typing | https://hla-net.eu/ |
| HLApers (Aguiar et al., 2020) | Genotyping and quantification of HLA expression from RNA-seq data | https://github.com/genevol-usp/HLApers |
| HLA-TAPAS (Luo et al., 2020) | Open-source Python pipeline for creation of reference panels and HLA association studies | https://github.com/immunogenomics/HLA-TAPAS |
| MergeReference (Cook and Han, 2017) | SNP2HLA compatible tool to concatenate multiple reference panels in order to gain accuracy during HLA imputation | http://software.buhmhan.com/MergeReference |
| pyHLA (Fan and Song, 2017) | Association analysis for HLA alleles in Python language | https://github.com/felixfan/PyHLA |