HLA*LA-HLA typing from linearly projected graph alignments.

ABSTRACT:

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.

SUBMITTER: Dilthey AT 

PROVIDER: S-EPMC6821427 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature