The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci.
Source text:
(Szolek et al., 2014) OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics.
Enables high precision Human Leukocyte Antigen (HLA)-typing even. POLYSOLVER…
Enables high precision Human Leukocyte Antigen (HLA)-typing even. POLYSOLVER uses relatively low coverage whole exome sequencing (WES) data and a subsequent mutation detection pipeline that is based…
Provides functions for association analysis, zygosity tests, and interaction…
Provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. PyHLA is a Python package which implements several methods for HLA association…
Permits to screen raw Illumina high-throughput sequencing (HTS) data for sample…
Permits to screen raw Illumina high-throughput sequencing (HTS) data for sample swaps for datasets where the Human Leukocyte Antigen (HLA) loci are covered. HLA-MA is based on the HLA typing result…
An algorithm for HLA type inference from next-generation sequencing data.…
An algorithm for HLA type inference from next-generation sequencing data. HLA-PRG outperforms existing methods by a wide margin and for the first time consistently achieves the accuracy of…
Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat…
Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat preprocesses the input genotype data, resolves genotyping ambiguities, translates alleles to a uniform resolution per…
Performs alignment of reads to human leukocyte antigen (HLA) sequences from the…
Performs alignment of reads to human leukocyte antigen (HLA) sequences from the international ImMunoGeneTics project (IMGT)/HLA database. HLAscan is an alignment-based multi-step HLA typing method…
Allows validation and analyses of human leukocyte antigen (HLA)-typed…
Allows validation and analyses of human leukocyte antigen (HLA)-typed population samples and their connection with the GENE[VA] database. HLA-NET is a platform conceived as an evolving set of tools…
Allows to discover and genotype sequence variants in large populations using…
Allows to discover and genotype sequence variants in large populations using pangenome graphs. Graphtyper is a population-scale genotype caller. The software locally realigns sequence reads from a…
A tool for HLA typing from NGS data based on read-mapping using a comprehensive…
A tool for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads.…
An efficient and accurate human leucocyte antigen (HLA) typing method using…
An efficient and accurate human leucocyte antigen (HLA) typing method using high-throughput sequencing data without the need of primer design for HLA loci. In the first step of the HLA-VBSeq…
Applies assembly, allele identification and allelic pair inference to short…
Applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C,…
A HLA genotyping algorithm based on integer linear programming, capable of…
A HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. OptiType significantly…
A NGS data analysis pipeline allowing user to make HLA alleles genotyping…
A NGS data analysis pipeline allowing user to make HLA alleles genotyping quickly and efficiently. HLATyphon supports all cDNA template of HLA locus A, B, C, DPA1, DPB1, DQA1, DQB1 and DRB1 in…
A tool algorithm named to discover the most probable pair of HLA alleles at…
A tool algorithm named to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring. PHLAT…
Gives high resolution results with whole genome, exome or very targeted DNA…
Gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data. Omixon Target HLA Typing offers high possible HLA typing precision using NGS data. There is no…
A software for HLA class I and II predictions from next-generation shotgun…
A software for HLA class I and II predictions from next-generation shotgun (NGS) sequence read data that supports direct read alignment and targeted assembly of sequence reads. This approach…
Provides a method for statistical refinement of low or intermediate resolution…
Provides a method for statistical refinement of low or intermediate resolution HLA (Human Leucocyte Antigen) data, when a full resolution training data set from a similar population is available. HLA…
Predicts HLA haplotype by hierarchically weighting reads and using an…
Predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bowtie, although any…
Allows to align DNA sequencing data. Gyper is a genotyper which provides a…
Allows to align DNA sequencing data. Gyper is a genotyper which provides a partial order graph which represents haplotypes. The software supports six Human Leukocyte Antigen (HLA) genes: HLA-A,…
By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.