Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.

Abstract

The positional Burrows-Wheeler transform (PBWT) data structure allows for efficient haplotype data matching and compression. Its performance makes it a powerful tool for bioinformatics. However, existing algorithms do not exploit parallelism due to inner dependencies. We introduce a new method to break the dependencies and show how to fully exploit modern multi-core processors. Source code and applications are available at https://github.com/rwk-unil/parallel_pbwt. Supplementary data are available at Bioinformatics Advances online.