The DOI matches its Crossref record; 129 of the 129 references it cites were found in a registry or an index.
A Primer on Metagenomics
Open accessAbstract
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.
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Cites
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Cited by
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The impact of next-generation sequencing on genomics
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“Currently de novo assembly with NGS data is generally limited to microbial genome projects (Metagenomics) due to the small bacterial genome size (Chistoserdova, 2010; Wooley et al., 2010).”
BackgroundThe Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
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Chapter 12: Human Microbiome Analysis
Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496
Metadata
- Authors
- Wooley, J. C., Godzik, A., & Friedberg, I.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-02-26
- Volume
- 6
- Issue
- 2
- Pages
- e1000667
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2006465310
- Cited by
- 688
- References
- 129
- FWCI
- 22.80
- Type
- journal article
- Language
- en
- Open access
- gold
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