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bioRxiv · 10.1101/453555

HLA*PRG:LA - HLA typing from linearly projected graph alignments

Dilthey, A. T.·Mentzer, A. J.·Carapito, R.·Cutland, C.·Cereb, N.·Madhi, S. A.·Rhie, A.·Koren, S.·Bahram, S.·McVean, G.·Phillippy, A. M.
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Abstract

SummaryHLA*PRG:LA implements a new graph alignment model for 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.\n\nAvailability and ImplementationHLA*PRG:LA is implemented in C++ and Perl and freely available from https://github.com/DiltheyLab/HLA-PRG-LA (GPL v3).\n\nContactalexander.dilthey@med.uni-duesseldorf.de\n\nSupplementary informationSupplementary data are available online.

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Dilthey, A. T., Mentzer, A. J., Carapito, R., Cutland, C., Cereb, N., Madhi, S. A., Rhie, A., Koren, S., Bahram, S., McVean, G., Phillippy, A. M.. 2018-10-26. HLA*PRG:LA - HLA typing from linearly projected graph alignments. https://doi.org/10.1101/453555

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