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Exploiting In-memory Systems for Genomic Data Analysis

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Bioinformatics and Biomedical Engineering (IWBBIO 2018)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10813))

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Abstract

With the increasing adoption of next generation sequencing technology in the medical practice, there is an increasing demand for faster data processing to gain immediate insights from the patient’s genome. Due to the extensive amount of genomic information and its big data nature, data processing takes long time and delays are often experienced. In this paper, we show how to exploit in-memory platforms for big genomic data analysis, with focus on the variant analysis workflow. We will determine where different in-memory techniques are used in the workflow and explore different memory-based strategies to speed up the analysis. Our experiments show promising results and encourage further research in this area, especially with the rapid advancement in memory and SSD technologies.

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Acknowledgments

This publication was supported by the Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST).

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Authors and Affiliations

  1. King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia

    Zeeshan Ali Shah, Mohamed El-Kalioby, Tariq Faquih, Shazia Subhani & Mohamed Abouelhoda

  2. Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia

    Zeeshan Ali Shah, Mohamed El-Kalioby, Tariq Faquih, Moustafa Shokrof, Shazia Subhani, Yasser Alnakhli, Hussain Aljafar & Mohamed Abouelhoda

  3. Department of Computing and Mathematics, University of Derby, Derby, UK

    Ashiq Anjum

Authors
  1. Zeeshan Ali Shah
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  2. Mohamed El-Kalioby
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  3. Tariq Faquih
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  4. Moustafa Shokrof
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  5. Shazia Subhani
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  6. Yasser Alnakhli
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  7. Hussain Aljafar
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  8. Ashiq Anjum
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  9. Mohamed Abouelhoda
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Corresponding author

Correspondence to Mohamed Abouelhoda .

Editor information

Editors and Affiliations

  1. University of Granada, Granada, Spain

    Ignacio Rojas

  2. University of Granada, Granada, Spain

    Francisco Ortuño

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Shah, Z.A. et al. (2018). Exploiting In-memory Systems for Genomic Data Analysis. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2018. Lecture Notes in Computer Science(), vol 10813. Springer, Cham. https://doi.org/10.1007/978-3-319-78723-7_35

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  • DOI: https://doi.org/10.1007/978-3-319-78723-7_35

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-78722-0

  • Online ISBN: 978-3-319-78723-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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