HLA*PRG:LA – HLA typing from linearly projected graph alignments
Dilthey A., Mentzer A., Carapito R., Cutland C., Cereb N., Madhi S., Rhie A., Koren S., Bahram S., McVean G., Phillippy A.
<h4>Summary:</h4> HLA*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. <h4>Availability and Implementation:</h4> HLA*PRG:LA is implemented in C++ and Perl and freely available from https://github.com/DiltheyLab/HLA-PRG-LA (GPL v3). <h4>Contact:</h4> firstname.lastname@example.org <h4>Supplementary information</h4> Supplementary data are available online.