Seedex: A genome sequencing accelerator for optimal alignments in subminimal space

Daichi Fujiki, Shunhao Wu, Nathan Ozog, Kush Goliya, David Blaauw, Satish Narayanasamy, Reetuparna Das

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

5 Citations (Scopus)

Abstract

Innovations in genome sequencing techniques are enabling remarkably fast and low cost production of raw genome data. As Moore's law tapers off, bottlenecks in genome sequencing are shifting to computational resources for mapping reads to reference DNA. This paper presents SeedEx, a read-alignment accelerator focused on the seed-extension step. SeedEx is based on the observation that only a small fraction of reads require large edit distance for alignment, hence an area efficient narrow-band seed-extension accelerator can suffice in practice. However, due to the highly error-sensitive nature of genomic workloads, guaranteeing optimality of alignment result is of cardinal importance. Towards this end, we propose a speculation-and-test based framework by using strict but powerful optimality checking mechanisms. We demonstrate SeedEx by an implementation on a cloud FPGA. SeedEx achieves 6.0× iso-area throughput speedup when compared to a banded Smith-Waterman baseline, and achieving 43.9 M seed extentions/s on AWS f1.2xlarge instance. Integration with BWA-MEM2 improves the execution time by 2.3×.

Original languageEnglish
Title of host publicationProceedings - 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020
PublisherIEEE Computer Society
Pages937-950
Number of pages14
ISBN (Electronic)9781728173832
DOIs
Publication statusPublished - 2020 Oct
Externally publishedYes
Event53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020 - Virtual, Athens, Greece
Duration: 2020 Oct 172020 Oct 21

Publication series

NameProceedings of the Annual International Symposium on Microarchitecture, MICRO
Volume2020-October
ISSN (Print)1072-4451

Conference

Conference53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020
Country/TerritoryGreece
CityVirtual, Athens
Period20/10/1720/10/21

Keywords

  • Accelerator
  • FPGA
  • Genome sequencing

ASJC Scopus subject areas

  • Hardware and Architecture

Fingerprint

Dive into the research topics of 'Seedex: A genome sequencing accelerator for optimal alignments in subminimal space'. Together they form a unique fingerprint.

Cite this