We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-y over the reads and the possibility to output both the best hits or all hits of a read. Designing the algorithm particularly for the GPU architecture, we were able to reach maximum core occupancy for several key steps. Our benchmarks show that PEANUT outperforms other state-ofthe-art mappers in terms of speed and sensitivity. The software is available at http: //peanut.readthedocs.org.
['Johannes Köster', 'Sven Rahmann']
Massively parallel read mapping on GPUs with PEANUT