title: 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.
authors.affiliation: Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Köster
authors.affiliation: Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Rahmann
keywords: Datastructure; GPU programming; Parallel algorithms; Read mapping