GenAx: A genome sequencing accelerator

Daichi Fujiki, Arun Subramaniyan, Tianjun Zhang, Yu Zeng, Reetuparna Das, David Blaauw, Satish Narayanasamy

研究成果: Conference contribution

43 被引用数 (Scopus)

抄録

Genomics can transform health-care through precision medicine. Plummeting sequencing costs would soon make genome testing affordable to the masses. Compute efficiency, however, has to improve by orders of magnitude to sequence and analyze the raw genome data. Sequencing software used today can take several hundreds to thousands of CPU hours to align reads to a reference sequence. This paper presents GenAx, an accelerator for read alignment, a time-consuming step in genome sequencing. It consists of a seeding and seed-extension accelerator. The latter is based on an innovative automata design that was designed from the ground-up to enable hardware acceleration. Unlike conventional Levenshtein automata, it is string independent and scales quadratically with edit distance, instead of string length. It supports critical features commonly used in sequencing such as affine gap scoring and traceback. GenAx provides a throughput of 4,058K reads/s for Illumina 101 bp reads. GenAx achieves 31.7× speedup over the standard BWA-MEM sequence aligner running on a 56-thread dual-socket 14-core Xeon E5 server processor, while reducing power consumption by 12× and area by 5.6×.

本文言語English
ホスト出版物のタイトルProceedings - 2018 ACM/IEEE 45th Annual International Symposium on Computer Architecture, ISCA 2018
出版社Institute of Electrical and Electronics Engineers Inc.
ページ69-82
ページ数14
ISBN(電子版)9781538659847
DOI
出版ステータスPublished - 2018 7月 19
外部発表はい
イベント45th ACM/IEEE Annual International Symposium on Computer Architecture, ISCA 2018 - Los Angeles, United States
継続期間: 2018 6月 22018 6月 6

出版物シリーズ

名前Proceedings - International Symposium on Computer Architecture
ISSN(印刷版)1063-6897

Conference

Conference45th ACM/IEEE Annual International Symposium on Computer Architecture, ISCA 2018
国/地域United States
CityLos Angeles
Period18/6/218/6/6

ASJC Scopus subject areas

  • ハードウェアとアーキテクチャ

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