Browsing by Subject "Sequence alignment acceleration"

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    GateKeeper-GPU: fast and accurate pre-alignment filtering in short read mapping
    (IEEE, 2021-06-24) Bingöl, Zülal; Alser, Mohammed; Mutlu, Onur; Öztürk, Özcan; Alkan, Can
    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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    GateKeeper-GPU: fast and accurate pre-alignment filtrering in short read mapping
    (IEEE, 2024-05) Bingol, Zülal; Alser, Mohammed; Mutlu, Onur; Öztürk, Özcan; Alkan, Can
    At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the similarities and differences between two sequences is still computationally expensive since approximate string matching techniques traditionally inherit dynamic programming algorithms with quadratic time and space complexity. We introduce GateKeeper-GPU, a fast and accurate pre-alignment filter that efficiently reduces the need for expensive sequence alignment. GateKeeper-GPU provides two main contributions: first, improving the filtering accuracy of GateKeeper (a lightweight pre-alignment filter), and second, exploiting the massive parallelism provided by the large number of GPU threads of modern GPUs to examine numerous sequence pairs rapidly and concurrently. By reducing the work, GateKeeper-GPU provides an acceleration of 2.9$\boldsymbol{\times}$ to sequence alignment and up to $1.4\boldsymbol{\times}$ speedup to the end-to-end execution time of a comprehensive read mapper (mrFAST). GateKeeper-GPU is available at https://github.com/BilkentCompGen/GateKeeper-GPU