HLA*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.