T. Thomas, J. Gilbert, F. Meyer, "Making the Most Out of Metagenomics - A Guide from Sampling to Data Analysis," Microbial Informatics and Experimentation, BioMed Central Ltd, 2011, . Also Preprint ANL/MCS-P1953-0911, September 2011. [pdf]
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 last 5-10 years and many research laboratories are actively engaged in it now. With the growing numbers of activities comes also a plethora of methodological knowledge and expertise that should guide the future developments in the field. This review aims to summarize the current metagenomic opinion, provide practical guidance and advice on sample processing, sequencing technology, assembly, annotation, experimental design, statistical analysis, data storage and sharing. As more metagenome data sets are generated the availability of standardized procedures as well as shared data storage and analysis become increasingly important to ensure output of individual projects can be assessed and compared.