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      Shouji: a fast and efficient pre-alignment filter for sequence alignment

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      Author(s)
      Alser, Mohammed
      Hassan, H.
      Kumar, A.
      Mutlu, Onur
      Alkan, Can
      Date
      2019
      Source Title
      Bioinformatics
      Print ISSN
      1367-4803
      Electronic ISSN
      ISSN 1460-2059
      Publisher
      Oxford University Press
      Volume
      35
      Issue
      21
      Pages
      4255 - 4263
      Language
      English
      Type
      Article
      Item Usage Stats
      142
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      249
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      Abstract
      The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern field-programmable gate array (FPGA) architectures to further boost the performance of our algorithm. Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8×. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step.
      Permalink
      http://hdl.handle.net/11693/53300
      Published Version (Please cite this version)
      https://doi.org/10.1093/bioinformatics/btz234
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