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HLA*LA—HLA typing from linearly projected graph alignments

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 lon...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821427/
https://www.ncbi.nlm.nih.gov/pubmed/30942877
http://dx.doi.org/10.1093/bioinformatics/btz235
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author 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
author_facet 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
author_sort Dilthey, Alexander T
collection PubMed
description 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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spelling pubmed-68214272019-11-04 HLA*LA—HLA typing from linearly projected graph alignments 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 Bioinformatics Applications Notes 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. Oxford University Press 2019-11-01 2019-04-03 /pmc/articles/PMC6821427/ /pubmed/30942877 http://dx.doi.org/10.1093/bioinformatics/btz235 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
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
HLA*LA—HLA typing from linearly projected graph alignments
title HLA*LA—HLA typing from linearly projected graph alignments
title_full HLA*LA—HLA typing from linearly projected graph alignments
title_fullStr HLA*LA—HLA typing from linearly projected graph alignments
title_full_unstemmed HLA*LA—HLA typing from linearly projected graph alignments
title_short HLA*LA—HLA typing from linearly projected graph alignments
title_sort hla*la—hla typing from linearly projected graph alignments
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821427/
https://www.ncbi.nlm.nih.gov/pubmed/30942877
http://dx.doi.org/10.1093/bioinformatics/btz235
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