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

doi:10.1109/CICC48029.2020.9075900

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 proceeding › Conference contribution

2 Citations (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 language	English
Title of host publication	2020 IEEE Custom Integrated Circuits Conference, CICC 2020
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781728160313
DOIs	https://doi.org/10.1109/CICC48029.2020.9075900
Publication status	Published - 2020 Mar
Externally published	Yes
Event	2020 IEEE Custom Integrated Circuits Conference, CICC 2020 - Boston, United States Duration: 2020 Mar 22 → 2020 Mar 25

Publication series

Name	Proceedings of the Custom Integrated Circuits Conference
Volume	2020-March
ISSN (Print)	0886-5930

Conference

Conference	2020 IEEE Custom Integrated Circuits Conference, CICC 2020
Country/Territory	United States
City	Boston
Period	20/3/22 → 20/3/25

Keywords

ASIC
DNA Sequencing
seed-extension

ASJC Scopus subject areas

Electrical and Electronic Engineering

Access to Document

10.1109/CICC48029.2020.9075900

Cite this

Wang, Z., Zhang, T., Fujiki, D., Subramaniyan, A., Wu, X., Yasuda, M., Miyoshi, S., Kawaminami, M., Das, R., Narayanasamy, S., & Blaauw, D. (2020). A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array. In 2020 IEEE Custom Integrated Circuits Conference, CICC 2020 [9075900] (Proceedings of the Custom Integrated Circuits Conference; Vol. 2020-March). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CICC48029.2020.9075900

A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array. / Wang, Zhehong; Zhang, Tianjun; Fujiki, Daichi et al.

2020 IEEE Custom Integrated Circuits Conference, CICC 2020. Institute of Electrical and Electronics Engineers Inc., 2020. 9075900 (Proceedings of the Custom Integrated Circuits Conference; Vol. 2020-March).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Wang, Z, Zhang, T, Fujiki, D, Subramaniyan, A, Wu, X, Yasuda, M, Miyoshi, S, Kawaminami, M, Das, R, Narayanasamy, S & Blaauw, D 2020, A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array. in 2020 IEEE Custom Integrated Circuits Conference, CICC 2020., 9075900, Proceedings of the Custom Integrated Circuits Conference, vol. 2020-March, Institute of Electrical and Electronics Engineers Inc., 2020 IEEE Custom Integrated Circuits Conference, CICC 2020, Boston, United States, 20/3/22. https://doi.org/10.1109/CICC48029.2020.9075900

Wang Z, Zhang T, Fujiki D, Subramaniyan A, Wu X, Yasuda M et al. A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array. In 2020 IEEE Custom Integrated Circuits Conference, CICC 2020. Institute of Electrical and Electronics Engineers Inc. 2020. 9075900. (Proceedings of the Custom Integrated Circuits Conference). doi: 10.1109/CICC48029.2020.9075900

@inproceedings{c248e3c6c3b24a9c89d35e7a41300b72,

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

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.",

keywords = "ASIC, DNA Sequencing, seed-extension",

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

note = "Publisher Copyright: {\textcopyright} 2020 IEEE.; 2020 IEEE Custom Integrated Circuits Conference, CICC 2020 ; Conference date: 22-03-2020 Through 25-03-2020",

year = "2020",

month = mar,

doi = "10.1109/CICC48029.2020.9075900",

language = "English",

series = "Proceedings of the Custom Integrated Circuits Conference",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

booktitle = "2020 IEEE Custom Integrated Circuits Conference, CICC 2020",

}

TY - GEN

T1 - A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array

AU - Wang, Zhehong

AU - Zhang, Tianjun

AU - Fujiki, Daichi

AU - Subramaniyan, Arun

AU - Wu, Xiao

AU - Yasuda, Makoto

AU - Miyoshi, Satoru

AU - Kawaminami, Masaru

AU - Das, Reetuparna

AU - Narayanasamy, Satish

AU - Blaauw, David

PY - 2020/3

Y1 - 2020/3

N2 - 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.

AB - 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.

KW - ASIC

KW - DNA Sequencing

KW - seed-extension

UR - http://www.scopus.com/inward/record.url?scp=85084456224&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85084456224&partnerID=8YFLogxK

U2 - 10.1109/CICC48029.2020.9075900

DO - 10.1109/CICC48029.2020.9075900

M3 - Conference contribution

AN - SCOPUS:85084456224

T3 - Proceedings of the Custom Integrated Circuits Conference

BT - 2020 IEEE Custom Integrated Circuits Conference, CICC 2020

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2020 IEEE Custom Integrated Circuits Conference, CICC 2020

Y2 - 22 March 2020 through 25 March 2020

ER -

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

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this