GateKeeper-GPU: fast and accurate pre-alignment filtering in short read mapping

Bingöl, ZülalAlser, MohammedMutlu, OnurÖztürk, ÖzcanAlkan, Can2022-02-082022-02-082021-06-24978-1-6654-1192-9http://hdl.handle.net/11693/77133Conference Name: 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)Date of Conference: 17-21 June 2021We 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.EnglishRead mappingPre-alignment filteringGPGPUSequence alignment accelerationGateKeeper-GPU: fast and accurate pre-alignment filtering in short read mappingConference Paper10.1109/IPDPSW52791.2021.00039978-1-6654-3577-2