HLA*LA-HLA typing from linearly projected graph alignments.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
26
10
2018
revised:
26
02
2019
accepted:
02
04
2019
pubmed:
4
4
2019
medline:
1
7
2020
entrez:
4
4
2019
Statut:
ppublish
Résumé
HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample. HLA*LA is implemented in C++ and Perl and freely available as a bioconda package or from https://github.com/DiltheyLab/HLA-LA (GPL v3). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30942877
pii: 5426702
doi: 10.1093/bioinformatics/btz235
pmc: PMC6821427
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4394-4396Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : European Research Council
ID : 294557
Pays : International
Organisme : Wellcome Trust
ID : 106289/Z/14/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
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