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Open Access Highly Accessed Review

Metagenomics - a guide from sampling to data analysis

Torsten Thomas1*, Jack Gilbert23 and Folker Meyer24

Author Affiliations

1 School of Biotechnology and Biomolecular Sciences & Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW 2052, Australia

2 Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA

3 Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA

4 Computation Institute, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA

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Microbial Informatics and Experimentation 2012, 2:3  doi:10.1186/2042-5783-2-3

Published: 9 February 2012

Abstract

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.

Keywords:
sampling; sequencing; assembly; binning; annotation; data storage; data sharing; DNA extraction; microbial ecology; microbial diversity