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HLA genotyping software tools | Whole-exome sequencing data analysis

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…
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POLYSOLVER
Desktop

POLYSOLVER POLYmorphic loci reSOLVER

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…

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PyHLA
Desktop

PyHLA

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…

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HLA-MA
Desktop

HLA-MA

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…

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HLA-PRG
Desktop

HLA-PRG

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…

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Hapl-o-Mat
Desktop

Hapl-o-Mat

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…

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HLAscan
Desktop

HLAscan

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…

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HLA-NET
Dataset

HLA-NET

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…

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Graphtyper
Desktop

Graphtyper

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…

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HLAreporter
Desktop

HLAreporter

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.…

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HLA-VBSeq
Desktop

HLA-VBSeq

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…

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ATHLATES
Desktop

ATHLATES

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,…

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OptiType
Desktop

OptiType

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…

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HLATyphon
Desktop

HLATyphon

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…

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PHLAT
Desktop

PHLAT

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…

TCLP
Dataset

TCLP TRON Cell Line Portal

Allows users to search and list gene expression values from a selected cell…

Allows users to search and list gene expression values from a selected cell line. TCLP integrates a catalog of cancer cell line annotations integrating human leukocyte antigen (HLA) type, HLA…

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Omixon Target…
Desktop

Omixon Target HLA Typing

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…

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HLAminer
Desktop

HLAminer

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…

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HLA Completion
Web
Desktop

HLA Completion

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…

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HLAforest
Desktop

HLAforest

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…

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HLA DB
Dataset

HLA DB HLA Database

Holds information about human leukocyte antigen (HLA). HLA DB is a repository…

Holds information about human leukocyte antigen (HLA). HLA DB is a repository system containing HLA haplotype data and disease-related information. This resource can be browse by two ways: (1) a…

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Gyper
Desktop

Gyper Graph genotYPER

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,…

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