PEANUT (ParallEl AligNment UTility) is an OpenCL based read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome. By exploiting the massive parallelism of modern graphics processors and a novel index datastructure, the authors say PEANUT achieves supreme sensitivity and speed compared to current state of the art read mappers like BWA MEM, Bowtie2 and RazerS3. PEANUT thereby allows to report both only the best hits or all hits.
A preprint of the original scientific paper “Massively Parallel Read Mapping on GPUs with PEANUT” by Johannes Koester and Sven Rahmann (Institute of Human Genetics, University Hospital Essen) is available at http://arxiv.org/abs/1403.1706
PEANUT is distributed under the MIT license as an open source Python3 software package. Filtration and validation where implemented in OpenCL, using the PyOpenCL package and postprocessing was implemented in Cython. Documentation and installation instructions are available at http://peanut.readthedocs.org