An introduction to the analysis of shotgun metagenomic data Public Deposited

http://ir.library.oregonstate.edu/concern/articles/xw42n948q

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at:  http://www.frontiersin.org/Plant_Science.

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  • Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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  • Sharpton, T. J. (2014) An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science, 5:209. doi:10.3389/fpls.2014.00209
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  • description.provenance : Made available in DSpace on 2014-08-18T22:20:05Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyIntroductionAnalysisShotgun.pdf: 1401253 bytes, checksum: eb853fe8042de73b5ed7367194349e25 (MD5) Previous issue date: 2014-06-16
  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-08-18T22:20:05Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyIntroductionAnalysisShotgun.pdf: 1401253 bytes, checksum: eb853fe8042de73b5ed7367194349e25 (MD5)
  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-08-18T22:19:52Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyIntroductionAnalysisShotgun.pdf: 1401253 bytes, checksum: eb853fe8042de73b5ed7367194349e25 (MD5)

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