Acceleration of the Pair-HMM Algorithm for DNA Variant Calling

Gowthami Jayashri Manikandan, Sitao Huang, Kyle Rupnow, Wen Mei W. Hwu, Deming Chen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In this project, we propose an SoC solution to accelerate the Pair-HMM's forward algorithm which is the key performance bottleneck in the GATK's HaplotypeCaller tool for DNA variant calling. We develop two versions of the Pair-HMM accelerator: one using High Level Synthesis (HLS), and another ring-based manual RTL implementation. We investigate the performance of the manual RTL design and HLS design in terms of design flexibility and overall run-time. We achieve a significant speed-up of up to 19x through the HLS implementation and speed-up of up to 95x through the RTL implementation of the algorithm.

Original languageEnglish (US)
Title of host publicationProceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Number of pages1
ISBN (Electronic)9781509023561
DOIs
StatePublished - Aug 16 2016
Event24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016 - Washington, United States
Duration: May 1 2016May 3 2016

Publication series

NameProceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016

Other

Other24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016
CountryUnited States
CityWashington
Period5/1/165/3/16

ASJC Scopus subject areas

  • Hardware and Architecture

Fingerprint Dive into the research topics of 'Acceleration of the Pair-HMM Algorithm for DNA Variant Calling'. Together they form a unique fingerprint.

  • Cite this

    Manikandan, G. J., Huang, S., Rupnow, K., Hwu, W. M. W., & Chen, D. (2016). Acceleration of the Pair-HMM Algorithm for DNA Variant Calling. In Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016 [7544765] (Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/FCCM.2016.42