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FastDRC: Fast and Scalable Genome Compression Based on Distributed and Parallel Processing

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Algorithms and Architectures for Parallel Processing (ICA3PP 2019)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11945))

Abstract

With the advent of next-generation sequencing technology, sequencing costs have fallen sharply compared to the previous sequencing technologies. Genomic big data has become the significant big data application. In the face of growing genomic data, its storage and migration face enormous challenges. Therefore, researchers have proposed a variety of genome compression algorithms, but these algorithms cannot meet the processing requirements for large amount of biological data and high processing speed. This manuscript proposes a parallel and distributed referential genome compression algorithm-Fast Distributed Referential Compression (FastDRC). This algorithm compresses a large number of genomic sequences in parallel under the Apache Hadoop distributed computing framework. Experiments show that the compression efficiency of the FastDRC is greatly improved when it compresses large quantities of genomic data. Moreover, FastDRC leads to the only distributed computing method known to us in the field of genome compression. The source code for FastDRC can be obtained from this link: https://github.com/GhostCCCatHenry/FastDRC.

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Acknowledgements

We would like to thank all reviewers for their valuable comments and suggestions to improve the quality of our manuscript.

Funding

This work was supported by the National Key R&D Program of China [2017YFB1401302, 2017YFB0202200], the National Natural Science Foundation of P. R. China [No. 61572260, 61872196], Outstanding Youth of Jiangsu Natural Science Foundation [BK20170100], Key R&D Program of Jiangsu [BE2017166], Postgraduate Research & Practice Innovation Program of Jiangsu Province [KYCX19_0906, KYCX19_0921], The Natural Science Foundation of the Jiangsu Higher Education Institutions of China [19KJD520006] and Modern Educational Technology Research Program of Jiangsu Province in 2019 [2019-R-67748].

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Authors and Affiliations

  1. School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China

    Yimu Ji, Houzhi Fang, Haichang Yao, Shuai Chen, Kui Li & Shangdong Liu

  2. School of Computer and Software, Nanjing Institute of Industry Technology, Nanjing, 210023, China

    Haichang Yao

  3. School of Software and Electrical Engineering, Swinburne University of Technology, Melbourne, 3122, Australia

    Jing He

  4. Institute of High Performance Computing and Big Data, Nanjing University of Posts and Telecommunications, Nanjing, 210003, China

    Yimu Ji

  5. Nanjing Center of HPC China, Nanjing, 210003, China

    Yimu Ji

  6. Jiangsu HPC and Intelligent Processing Engineer Research Center, Nanjing, 210003, China

    Yimu Ji

Authors
  1. Yimu Ji
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  2. Houzhi Fang
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  3. Haichang Yao
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  4. Jing He
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  5. Shuai Chen
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  6. Kui Li
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  7. Shangdong Liu
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Corresponding author

Correspondence to Haichang Yao .

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Editors and Affiliations

  1. Department of Computer Science and Software Engineering, Swinburne University of Technology, Hawthorn, Melbourne, VIC, Australia

    Sheng Wen

  2. School of Computer Science, The University of Sydney, Camperdown, NSW, Australia

    Albert Zomaya

  3. Department of Computer Science, St. Francis Xavier University, Antigonish, NS, Canada

    Laurence T. Yang

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Ji, Y. et al. (2020). FastDRC: Fast and Scalable Genome Compression Based on Distributed and Parallel Processing. In: Wen, S., Zomaya, A., Yang, L.T. (eds) Algorithms and Architectures for Parallel Processing. ICA3PP 2019. Lecture Notes in Computer Science(), vol 11945. Springer, Cham. https://doi.org/10.1007/978-3-030-38961-1_27

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  • DOI: https://doi.org/10.1007/978-3-030-38961-1_27

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-38960-4

  • Online ISBN: 978-3-030-38961-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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