Acceleration of the Pair-HMM Algorithm for DNA Variant Calling

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

doi:10.1109/FCCM.2016.42

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 proceeding › Conference 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 language	English (US)
Title of host publication	Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016
Publisher	Institute of Electrical and Electronics Engineers Inc.
Number of pages	1
ISBN (Electronic)	9781509023561
DOIs	https://doi.org/10.1109/FCCM.2016.42
State	Published - Aug 16 2016
Event	24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016 - Washington, United States Duration: May 1 2016 → May 3 2016

Publication series

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

Other

Other	24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016
Country	United States
City	Washington
Period	5/1/16 → 5/3/16

ASJC Scopus subject areas

Hardware and Architecture

Access to Document

10.1109/FCCM.2016.42

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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

Acceleration of the Pair-HMM Algorithm for DNA Variant Calling. / Manikandan, Gowthami Jayashri; Huang, Sitao; Rupnow, Kyle; Hwu, Wen Mei W.; Chen, Deming.

Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016. Institute of Electrical and Electronics Engineers Inc., 2016. 7544765 (Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Manikandan, GJ, Huang, S, Rupnow, K, Hwu, WMW & 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., 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016, Washington, United States, 5/1/16. https://doi.org/10.1109/FCCM.2016.42

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

Manikandan, Gowthami Jayashri ; Huang, Sitao ; Rupnow, Kyle ; Hwu, Wen Mei W. ; Chen, Deming. / Acceleration of the Pair-HMM Algorithm for DNA Variant Calling. Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016. Institute of Electrical and Electronics Engineers Inc., 2016. (Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016).

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