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Health Informatics Data Analysis pp 73–87Cite as

Metagenomics for Monitoring Environmental Biodiversity: Challenges, Progress, and Opportunities

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Abstract

Metagenomics, as the genomic analysis of DNA materials from environmental samples containing multiple genomic components, is attracting more and more interests due to its wide applications on microbial, cancer, and immunology researches. This chapter provides an overview on the topic covering the major steps involved in data collection, processing, and analysis. We describe and discuss experiment design, sample processing and quality control, sequencing and assembly, annotation, and downstream analyses. For each step, we summarize the current points of views, key issues, and popular tools. A step-by-step tutorial is then given using the popular QIIME pipeline on a bacterial 16S rRNA study case, which would benefit new scientists of the field for the startup of a successful metagenome project.

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Author information

Authors and Affiliations

  1. The Joint Department of Biomedical Engineering Department, Georgia Institute of Technology, Emory University, Atlanta, USA

    Raghu Chandramohan, Cheng Yang & May D. Wang

  2. Peking University, Beijing, China

    Raghu Chandramohan, Cheng Yang & May D. Wang

  3. Research Center for Biomedical Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, China

    Yunpeng Cai

Authors
  1. Raghu Chandramohan
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  2. Cheng Yang
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  3. Yunpeng Cai
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  4. May D. Wang
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Corresponding author

Correspondence to May D. Wang .

Editor information

Editors and Affiliations

  1. Digital Biology Laboratory, Computer Science Department, University of Missouri-Columbia, Columbia, Missouri, USA

    Dong Xu

  2. Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA

    May D. Wang

  3. College of Computer Science and Technology, Jilin University, Changchun, China

    Fengfeng Zhou

  4. Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China

    Yunpeng Cai

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Chandramohan, R., Yang, C., Cai, Y., Wang, M.D. (2017). Metagenomics for Monitoring Environmental Biodiversity: Challenges, Progress, and Opportunities. In: Xu, D., Wang, M., Zhou, F., Cai, Y. (eds) Health Informatics Data Analysis. Health Information Science. Springer, Cham. https://doi.org/10.1007/978-3-319-44981-4_5

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  • DOI: https://doi.org/10.1007/978-3-319-44981-4_5

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