Massively parallel read mapping on GPUs with the q-group index and PEANUT
Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Germany
PeerJ 2:e606, 2014
@article{koster2014massively,
title={Massively parallel read mapping on GPUs with the q-group index and PEANUT},
author={Koster, Johannes and Rahmann, Sven},
year={2014}
}
We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity.
October 20, 2014 by hgpu
