Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK

Wertenbroek, Rick (School of Management and Engineering Vaud, HES-SO // University of Applied Sciences Western Switzerland) ; Thoma, Yann (School of Management and Engineering Vaud, HES-SO // University of Applied Sciences Western Switzerland)

The Pair-HMM forward algorithm is an essential algorithm found in many genomic related analyses. The high number of floating point operations in the algorithm makes it one of the main contributors to the compute time of analysis pipelines. To speed-up computations we propose an FPGA-based hardware accelerator for the Amazon AWS F1 Cloud platform. The accelerator is open source and has been tested within the popular Genomic Analysis Toolkit (GATK) pipeline. The accelerator achieved up to 15 × speed-up against the software implementation when used in-pipeline. The accelerator has also been tested in the experimental Spark (distributed) version of the GATK HaplotypeCaller tool. An in-depth analysis of the compute time contributions allowed to point out the main bottlenecks for accelerators in the GATK pipeline, resulting in a hybrid CPU-FPGA solution to best exploit both resources.


Keywords:
Conference Type:
full paper
Faculty:
Ingénierie et Architecture
School:
HEIG-VD
Institute:
ReDS - Reconfigurable & embedded Digital Systems
Publisher:
San Diego, CA, USA, 18-21 November 2019
Date:
2019-11
San Diego, CA, USA
18-21 November 2019
Pagination:
8 p.
Published in:
Proceedings of 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 18-21 November 2019, San Diego, CA, USA
DOI:
ISBN:
978-1-7281-1867-3
Appears in Collection:



 Record created 2020-03-25, last modified 2020-10-27

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