HLALA—HLA typing from linearly projected graph alignments

Abstract Summary 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;...

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Bibliographic Details
Published in:Bioinformatics Vol. 35; no. 21; pp. 4394 - 4396
Main Authors: Dilthey, Alexander T, Mentzer, Alexander J, Carapito, Raphael, Cutland, Clare, Cereb, Nezih, Madhi, Shabir A, Rhie, Arang, Koren, Sergey, Bahram, Seiamak, McVean, Gil, Phillippy, Adam M
Format: Journal Article
Language:English
Published: England Oxford University Press 01.11.2019
Oxford University Press (OUP)
Subjects:
Applications Notes
Genome
High-Throughput Nucleotide Sequencing
Histocompatibility Testing
Humans
Immunology
Life Sciences
Sequence Analysis, DNA
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary:Abstract Summary 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. Availability and implementation 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 information Supplementary data are available at Bioinformatics online.
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PMCID: PMC6821427
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btz235