GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Özcan Öztürk, Can Alkan
Abstract
We introduce GateKeeper-GPU, a fast and accurate pre-alignment filter that efficiently reduces the need for expensive sequence alignment. GateKeeper-GPU improves the filtering accuracy of GateKeeper, and by exploiting the massive parallelism provided by GPU threads it concurrently examines numerous sequence pairs rapidly. GateKeeper-GPU is available at https://github.com/BilkentCompGen/GateKeeper-GPU. Please refer to the preprint at arXiv:2103.14978 for more information.
Topics & Concepts
Computer scienceParallel computingCUDASequence (biology)Filter (signal processing)Parallelism (grammar)General-purpose computing on graphics processing unitsComputer graphics (images)GraphicsComputer visionGeneticsBiologyGenomics and Phylogenetic StudiesAlgorithms and Data CompressionMachine Learning in Bioinformatics