A bioinformatician's guide to metagenomics

Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008) A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews, 72 4: 557-578. doi:10.1128/MMBR.00009-08

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Author Kunin, V.
Copeland, A.
Lapidus, A.
Mavromatis, K.
Hugenholtz, P.
Title A bioinformatician's guide to metagenomics
Journal name Microbiology and Molecular Biology Reviews   Check publisher's open access policy
ISSN 1092-2172
Publication date 2008-12
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1128/MMBR.00009-08
Open Access Status File (Publisher version)
Volume 72
Issue 4
Start page 557
End page 578
Total pages 12
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Language eng
Abstract As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collection: School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 162 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 179 times in Scopus Article | Citations
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Created: Fri, 24 Jun 2011, 15:27:23 EST by Professor Philip Hugenholtz on behalf of School of Chemistry & Molecular Biosciences