HLA*LA-HLA typing from linearly projected graph alignments.
Dilthey AT., Mentzer AJ., Carapito R., Cutland C., Cereb N., Madhi SA., Rhie A., Koren S., Bahram S., McVean G., Phillippy AM.
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.