Journal
JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
Volume 25, Issue 1, Pages 71-81Publisher
SCIENCE PRESS
DOI: 10.1007/s11390-010-9306-4
Keywords
metagenomics; next-generation sequencing (NGS); taxonomic/functional profiling; statistical approaches; comparative metagenomics
Funding
- NIH [1R01HG004908-01]
- NSF of USA [DBI-0845685]
- Gordon and Betty Moore Foundation
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG004908] Funding Source: NIH RePORTER
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Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and,discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.
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