HLA*PRG:LA – HLA typing from linearly projected graph alignments [article]

Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A. Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean, Adam M Phillippy
2018 bioRxiv   pre-print
AbstractSummary: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
more » ... r sample.Availability and Implementation:HLA*PRG:LA is implemented in C++ and Perl and freely available from https://github.com/DiltheyLab/HLA-PRG-LA (GPL v3).Contact:alexander.dilthey@med.uni-duesseldorf.deSupplementary informationSupplementary data are available online.
doi:10.1101/453555 fatcat:juirt2e2qzgrhidqmeyonc6ty4