GPU Acceleration of Advanced k-mer Counting for Computational Genomics

Huiren Li; Anand Ramachandran; Deming Chen

doi:10.1109/ASAP.2018.8445084

GPU Acceleration of Advanced k-mer Counting for Computational Genomics

Huiren Li, Anand Ramachandran, Deming Chen

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

Abstract

k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. Compared to KMC2 running on a single CPU thread, our implementation using the GPU achieved $\mathbf{4.03x}$ speedup when using one CPU thread, and $\mathbf{5.88x}$ speedup when using four CPU threads. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations.

Original language	English (US)
Title of host publication	2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Print)	9781538674796
DOIs	https://doi.org/10.1109/ASAP.2018.8445084
State	Published - Aug 23 2018
Event	29th IEEE International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018 - Milan, Italy Duration: Jul 10 2018 → Jul 12 2018

Publication series

Name	Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors
Volume	2018-July
ISSN (Print)	1063-6862

Other

Other	29th IEEE International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018
Country/Territory	Italy
City	Milan
Period	7/10/18 → 7/12/18

ASJC Scopus subject areas

Hardware and Architecture
Computer Networks and Communications

Online availability

10.1109/ASAP.2018.8445084

Library availability

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Li, H., Ramachandran, A., & Chen, D. (2018). GPU Acceleration of Advanced k-mer Counting for Computational Genomics. In 2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018 Article 8445084 (Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors; Vol. 2018-July). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ASAP.2018.8445084

GPU Acceleration of Advanced k-mer Counting for Computational Genomics. / Li, Huiren; Ramachandran, Anand; Chen, Deming.
2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018. Institute of Electrical and Electronics Engineers Inc., 2018. 8445084 (Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors; Vol. 2018-July).

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

Li, H, Ramachandran, A & Chen, D 2018, GPU Acceleration of Advanced k-mer Counting for Computational Genomics. in 2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018., 8445084, Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors, vol. 2018-July, Institute of Electrical and Electronics Engineers Inc., 29th IEEE International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018, Milan, Italy, 7/10/18. https://doi.org/10.1109/ASAP.2018.8445084

Li H, Ramachandran A, Chen D. GPU Acceleration of Advanced k-mer Counting for Computational Genomics. In 2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018. Institute of Electrical and Electronics Engineers Inc. 2018. 8445084. (Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors). doi: 10.1109/ASAP.2018.8445084

Li, Huiren ; Ramachandran, Anand ; Chen, Deming. / GPU Acceleration of Advanced k-mer Counting for Computational Genomics. 2018 IEEE 29th International Conference on Application-Specific Systems, Architectures and Processors, ASAP 2018. Institute of Electrical and Electronics Engineers Inc., 2018. (Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors).

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abstract = "k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. Compared to KMC2 running on a single CPU thread, our implementation using the GPU achieved $\mathbf{4.03x}$ speedup when using one CPU thread, and $\mathbf{5.88x}$ speedup when using four CPU threads. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations.",

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AB - k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. Compared to KMC2 running on a single CPU thread, our implementation using the GPU achieved $\mathbf{4.03x}$ speedup when using one CPU thread, and $\mathbf{5.88x}$ speedup when using four CPU threads. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations.

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GPU Acceleration of Advanced k-mer Counting for Computational Genomics

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