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

Mohammed Alser1,2,3, Hasan Hassan1, Akash Kumar2

  • 1Computer Science Department, ETH Zürich, Zürich, Switzerland.

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|March 30, 2019
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Summary
This summary is machine-generated.

Shouji, a novel pre-alignment filter, dramatically speeds up genome analysis by accurately identifying common subsequences. Its FPGA accelerator offers significant performance gains for sequence alignment tasks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Massive sequencing data generation strains current computational resources.
  • Efficient sequence alignment is critical for genomic data analysis.
  • Existing algorithms struggle to keep pace with data volume.

Purpose of the Study:

  • To reduce the execution time of short sequence alignment.
  • To introduce Shouji, a hardware/software co-designed pre-alignment filter.
  • To leverage hardware acceleration for bioinformatics pipelines.

Main Methods:

  • Developed Shouji, a highly parallel and accurate pre-alignment filter.
  • Designed a hardware accelerator using Field-Programmable Gate Array (FPGA) architectures.
  • Integrated Shouji with five state-of-the-art sequence aligners.

Main Results:

  • Shouji improves pre-alignment filtering accuracy by up to two orders of magnitude.
  • The FPGA accelerator is up to three orders of magnitude faster than CPU implementation.
  • Integration of Shouji reduced execution time of aligners by up to 18.8×.

Conclusions:

  • Shouji significantly accelerates sequence alignment without sacrificing accuracy or capabilities.
  • Hardware acceleration via FPGAs offers substantial performance improvements for genomic data processing.
  • Shouji is adaptable to various bioinformatics pipelines requiring sequence alignment.