Acceleration of Short Read Alignment with Runtime Reconfiguration

Ho Cheung Ng, Shuanglong Liu, Izaak Coleman, Ringo S.W. Chu, Man Chung Yue, Wayne Luk

Research output: Chapter in book / Conference proceedingConference article published in proceeding or bookAcademic researchpeer-review

1 Citation (Scopus)

Abstract

Recent advancements in the throughput of next-generation sequencing machines pose a huge computational challenge in analyzing the massive quantities of sequenced data produced. A critical initial step of genomic data analysis is short read alignment, which is a bottleneck in the analysis workflow. This paper explores the use of a reconfigurable architecture to accelerate this process, based on the seed-And-extend model of Bowtie2. In the proposed approach, complete information available in sequencing data is integrated into an FPGA alignment pipeline for biologically accurate runtime acceleration. Experimental results show that our architecture achieves a similar alignment rate compared to Bowtie2, mapping reads around twice as fast. Particularly, the alignment time is reduced from 50 minutes to 26 minutes when processing 300M reads.

Original languageEnglish
Title of host publicationProceedings - 2020 International Conference on Field-Programmable Technology, ICFPT 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages256-262
Number of pages7
ISBN (Electronic)9780738105185
DOIs
Publication statusPublished - Dec 2020
Event2020 International Conference on Field-Programmable Technology, ICFPT 2020 - Maui, United States
Duration: 7 Dec 20208 Dec 2020

Publication series

NameProceedings - 2020 International Conference on Field-Programmable Technology, ICFPT 2020

Conference

Conference2020 International Conference on Field-Programmable Technology, ICFPT 2020
Country/TerritoryUnited States
CityMaui
Period7/12/208/12/20

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computational Theory and Mathematics
  • Computer Networks and Communications
  • Hardware and Architecture

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