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

研究成果: Conference contribution

12 被引用数 (Scopus)

抄録

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×.

本文言語English
ホスト出版物のタイトルProceedings - 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020
出版社IEEE Computer Society
ページ937-950
ページ数14
ISBN(電子版)9781728173832
DOI
出版ステータスPublished - 2020 10月
外部発表はい
イベント53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020 - Virtual, Athens, Greece
継続期間: 2020 10月 172020 10月 21

出版物シリーズ

名前Proceedings of the Annual International Symposium on Microarchitecture, MICRO
2020-October
ISSN(印刷版)1072-4451

Conference

Conference53rd Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2020
国/地域Greece
CityVirtual, Athens
Period20/10/1720/10/21

ASJC Scopus subject areas

  • ハードウェアとアーキテクチャ

フィンガープリント

「Seedex: A genome sequencing accelerator for optimal alignments in subminimal space」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル