HLAreporter statistics

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Associated diseases

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HLAreporter specifications

Information


Unique identifier OMICS_08350
Name HLAreporter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wanling Yang <>

Publication for HLAreporter

HLAreporter in publications

 (3)
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] several tools have been developed to obtain hla allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and rna sequencing data), including optitype, polysolver, phlat, hlareporter, hlaforest, hlaminer, and seq2hla. we have tested 961 whole‐exome data from the 1000 genomes project to evaluate the accuracy of these programs. among these algorithms, optitype showed […]

PMCID: 5733459
PMID: 29326702
DOI: 10.3389/fimmu.2017.01815

[…] indicating which alleles best align to each read. using this matrix and integer linear programming, the best allele combination is selected by maximizing the number of reads mapping to each gene., hlareporter version 1.03 () begins by filtering the ngs reads, which is done by mapping them to a reference sequence panel. this reference set is at intermediate level of resolution consisting […]

PMCID: 4869273
PMID: 27188848
DOI: 10.1186/s12864-016-2688-0

[…] the genotyping process. the complex polymorphic structure of the mhc class i locus in some species also hampers approaches including exclusively de novo assembly of reads as implemented e.g., in the hlareporter typing tool []. in cattle, the problem with de novo assembly is further acerbated by the strong sequence similarity between genes []. dudley et al. [] developed an rnaseq-based method […]


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HLAreporter institution(s)
Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong

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