GateKeeper-GPU: fast and accurate pre-alignment filtering in short read mapping
Date
2021-06-24
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Source Title
IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)
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Publisher
IEEE
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Pages
209
Language
English
Type
Conference Paper
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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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Keywords
Read mapping, Pre-alignment filtering, GPGPU, Sequence alignment acceleration