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

ABSTRACT: 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.

SUBMITTER: Koster J

PROVIDER: S-EPMC4184027 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Köster Johannes J Rahmann Sven S

PeerJ 20140930

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 ...[more]

PMID: 25289191

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