12958

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Johannes Koster, Sven Rahmann
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}

}

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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.
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