A 2.46M Reads/s seed-extension accelerator for next-generation sequencing using a string-independent PE 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/JSSC.2020.3023822

A 2.46M Reads/s seed-extension accelerator for next-generation sequencing using a string-independent PE 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: Contribution to journal › Article › peer-review

Abstract

Advances in DNA-sequencing technology have far outpaced Moore's law, imposing significant challenges on the computationally intensive secondary analysis in the sequencing pipeline. An accelerator for seed extension, a critical and computationally intensive step in genome sequencing, is proposed. The accelerator, implementing a string-independent automata, consists of a triangular array of 25× 2 custom-designed processing elements. It performs 2.46 million reads per second (MRPS), achieving a 1581× improvement in power efficiency and 165.5 × smaller silicon footprint compared to a system setting with dual-socket Xeon E5-2697 v3 server processors.

Original language	English
Article number	9204364
Pages (from-to)	824-833
Number of pages	10
Journal	IEEE Journal of Solid-State Circuits
Volume	56
Issue number	3
DOIs	https://doi.org/10.1109/JSSC.2020.3023822
Publication status	Published - 2021 Mar
Externally published	Yes

Keywords

Application-specified integrated circuit (ASIC)
DNA sequencing
Levenshtein edits
seed-extension
string-independent automata

ASJC Scopus subject areas

Electrical and Electronic Engineering

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10.1109/JSSC.2020.3023822

Cite this

Wang, Z., Zhang, T., Fujiki, D., Subramaniyan, A., Wu, X., Yasuda, M., Miyoshi, S., Kawaminami, M., Das, R., Narayanasamy, S., & Blaauw, D. (2021). A 2.46M Reads/s seed-extension accelerator for next-generation sequencing using a string-independent PE array. IEEE Journal of Solid-State Circuits, 56(3), 824-833. Article 9204364. https://doi.org/10.1109/JSSC.2020.3023822

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abstract = "Advances in DNA-sequencing technology have far outpaced Moore's law, imposing significant challenges on the computationally intensive secondary analysis in the sequencing pipeline. An accelerator for seed extension, a critical and computationally intensive step in genome sequencing, is proposed. The accelerator, implementing a string-independent automata, consists of a triangular array of 25× 2 custom-designed processing elements. It performs 2.46 million reads per second (MRPS), achieving a 1581× improvement in power efficiency and 165.5 × smaller silicon footprint compared to a system setting with dual-socket Xeon E5-2697 v3 server processors.",

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AU - Subramaniyan, Arun

AU - Wu, Xiao

AU - Yasuda, Makoto

AU - Miyoshi, Satoru

AU - Kawaminami, Masaru

AU - Das, Reetuparna

AU - Narayanasamy, Satish

AU - Blaauw, David

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AB - Advances in DNA-sequencing technology have far outpaced Moore's law, imposing significant challenges on the computationally intensive secondary analysis in the sequencing pipeline. An accelerator for seed extension, a critical and computationally intensive step in genome sequencing, is proposed. The accelerator, implementing a string-independent automata, consists of a triangular array of 25× 2 custom-designed processing elements. It performs 2.46 million reads per second (MRPS), achieving a 1581× improvement in power efficiency and 165.5 × smaller silicon footprint compared to a system setting with dual-socket Xeon E5-2697 v3 server processors.

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A 2.46M Reads/s seed-extension accelerator for next-generation sequencing using a string-independent PE array

Abstract

Keywords

ASJC Scopus subject areas

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