SMEM++: A pipelined and time-multiplexed SMEM seeding accelerator for genome sequencing

Jason Cong, Licheng Guo, Po-Tsang Huang, Peng Wei, Tianhe Yu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Next-generation sequencing motivates the researchof FPGA acceleration for genome sequencing algorithms. Therecently developed quadratic-time SMEM seeding algorithmbecomes a time-consuming computation kernel in genomesequencing, but it has not been well studied. The fundamentalchallenge of accelerating the SMEM algorithm is to handle itslarge volume of random memory accesses. While the state-ofthe-art SMEM accelerator attempts sacrifices the performanceof individual processing elements to maximize the task-levelparallelism, this methodology suffers a serious resource underutilizationissue. Therefore, we propose SMEM++, a pipelinedand time-multiplexed FPGA accelerator for SMEM algorithm.SMEM++ adopts the canonical non-blocking pipelinemethodology and implements a fully pipelined acceleratorwith initiation interval equal to one. Moreover, we designa communication interface adapter to make the acceleratorcompatible to the target platform interface and increase itsportability. Experiments on the Intel HARPv2 platform showthat SMEM++ outperforms the original software by 24x, andoutperforms the state-of-the-art SMEM accelerator design by6.3x, with 43% less logic resource usage.

Original languageEnglish
Title of host publicationProceedings - 2018 International Conference on Field-Programmable Logic and Applications, FPL 2018
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages210-214
Number of pages5
ISBN (Electronic)9781538685174
DOIs
StatePublished - 9 Nov 2018
Event28th International Conference on Field-Programmable Logic and Applications, FPL 2018 - Dublin, Ireland
Duration: 26 Aug 201830 Aug 2018

Publication series

NameProceedings - 2018 International Conference on Field-Programmable Logic and Applications, FPL 2018

Conference

Conference28th International Conference on Field-Programmable Logic and Applications, FPL 2018
CountryIreland
CityDublin
Period26/08/1830/08/18

Keywords

  • FPGA Acceleration
  • Genome Sequencing
  • SMEM Algorithm

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    Cong, J., Guo, L., Huang, P-T., Wei, P., & Yu, T. (2018). SMEM++: A pipelined and time-multiplexed SMEM seeding accelerator for genome sequencing. In Proceedings - 2018 International Conference on Field-Programmable Logic and Applications, FPL 2018 (pp. 210-214). [8533495] (Proceedings - 2018 International Conference on Field-Programmable Logic and Applications, FPL 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/FPL.2018.00042