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R/V Helix out of Woods Hole, photo by A. Murat Eren

Welcome to STAMPS 2015

Strategies and Techniques for Analyzing Microbial Population Structure

David Mark Welch Marine Biological Laboratory
Mitch Sogin Marine Biological Laboratory

Course Date: August 5 - August 15, 2015

Twitter hash: #STAMPS15

Deep DNA sequencing using massively-parallel, next-generation technology has enabled nearly comprehensive environmental surveys that can describe the different kinds of microbes in a community and their relative abundance. These descriptions of richness and evenness make possible estimates of microbial diversity, but the size of the required data sets pose enormous computational challenges. The rapidly expanding flow of information from next generation DNA sequencing platforms has fueled healthy debate about best practices for data analysis while at the same time building a user demand for tools that can address important ecological questions. The STAMPS course will promote dialogue and the exchange of ideas between experts in analysis of metagenomic data and offer interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics.

Topics to be covered include but are not limited to next-generation strategies for analysis of microbial communities; acquisition and organization of next generation sequence data; principles of quality control of sequence data; the theory of cluster and rarefaction analyses; taxonomic assignments for high-throughput data; statistical models for estimating microbial diversity; microbial community comparison methodology and metrics; and analysis of shotgun metagenomic data. The lectures will be augmented by a computer laboratory where students will have the opportunity to use state of the art facilities to test theoretical concepts described in the lectures series.


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