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Updated: Aug 7, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching
Rick Wertenbroek1,2, Ioannis Xenarios2, Yann Thoma1
1School of Engineering and Management Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains 1401, Switzerland.
Summary:
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.
Availability And Implementation:
Source code and applications are available at https://github.com/rwk-unil/parallel_pbwt.
Supplementary Information:
Supplementary data are available at Bioinformatics Advances online.
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