A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array

Zhehong Wang, Tianjun Zhang, Daichi Fujiki, Arun Subramaniyan, Xiao Wu, Makoto Yasuda, Satoru Miyoshi, Masaru Kawaminami, Reetuparna Das, Satish Narayanasamy, David Blaauw

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

1 Citation (Scopus)

Abstract

We present an accelerator for seed-extension, a critical and computational intensive step in genome sequencing. The accelerator consists of a triangular array of 25×25 custom design processing elements implementing a string-independent automata. It achieves 2.46M reads/s, a 1800x performance improvement, and 27x smaller silicon footprint compared to a Xeon E5420.

Original languageEnglish
Title of host publication2020 IEEE Custom Integrated Circuits Conference, CICC 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781728160313
DOIs
Publication statusPublished - 2020 Mar
Externally publishedYes
Event2020 IEEE Custom Integrated Circuits Conference, CICC 2020 - Boston, United States
Duration: 2020 Mar 222020 Mar 25

Publication series

NameProceedings of the Custom Integrated Circuits Conference
Volume2020-March
ISSN (Print)0886-5930

Conference

Conference2020 IEEE Custom Integrated Circuits Conference, CICC 2020
Country/TerritoryUnited States
CityBoston
Period20/3/2220/3/25

Keywords

  • ASIC
  • DNA Sequencing
  • seed-extension

ASJC Scopus subject areas

  • Electrical and Electronic Engineering

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