Book chapter
Analysis Methods for Shotgun Metagenomics
Theoretical and Applied Aspects of Systems Biology, pp 71-112
01 Jan 2018
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The development of whole metagenome shotgun sequencing (WGS) has enabled the precise characterization of taxonomic diversity and functional capabilities of microbial communities in situ while obviating organism isolation and cultivation procedures. WGS created with second- and third-generation sequencing technologies will generate millions of reads and tens (or hundreds) of gigabytes of information about the organisms under investigation. Despite containing an immense amount of information, the reads are unorganized and unlabeled, leading to a significant challenge in discerning from which genome a read originated. Thus, analysis of WGS data necessitates first determining community structure and function from the raw reads before the focus can shift to making multi-sample comparisons. A typical WGS workflow consists of read assignment (taxonomic binning and classification), preprocessing techniques (normalization, dimensionality reduction), exploratory approaches (feature selection and extraction, ordination), statistical inference (regression, constrained ordination, differential abundance analysis), and machine learning. The following chapter provides an overview of these analytical approaches (including challenges and possible pitfalls that may be encountered by researchers) as well as steps toward their solutions. Relevant software packages and resources are also discussed.
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Details
- Title
- Analysis Methods for Shotgun Metagenomics
- Creators
- Stephen Woloszynek - Drexel UniversityZhengqiao Zhao - Drexel UniversityGregory Ditzler - University of ArizonaJacob R. Price - Drexel UniversityErin R. Reichenberger - Eastern Regional Research CenterYemin Lan - University of PennsylvaniaJian Chen - Drexel UniversityJoshua Earl - Drexel UniversitySaeed Keshani Langroodi - Drexel UniversityGarth Ehrlich - Drexel UniversityGail Rosen - Drexel University
- Contributors
- FAB DaSilva (Editor)N Carels (Editor)F P Silva (Editor)
- Publication Details
- Theoretical and Applied Aspects of Systems Biology, pp 71-112
- Series
- Computational Biology Series
- Publisher
- Springer Nature; DORDRECHT
- Number of pages
- 42
- Resource Type
- Book chapter
- Language
- English
- Academic Unit
- Microbiology and Immunology; Electrical and Computer Engineering; Civil, Architectural, and Environmental Engineering
- Web of Science ID
- WOS:000444707500007
- Other Identifier
- 991019168717704721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biology
- Mathematical & Computational Biology