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

Date

2021-06-24

Authors

Bingöl, Zülal
Alser, Mohammed
Mutlu, Onur
Öztürk, Özcan
Alkan, Can

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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.

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IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

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IEEE

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Published Version (Please cite this version)

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English