Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS)

Course Information

Watch STAMPS WebinarCourse Dates: Not offered in 2021

2019 Lecture Schedule

Course Website

Directors: Mihai Pop, University of Maryland; and Tracy Teal, Dryad

Course Description

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.

The course is designed for established investigators, postdoctoral fellows and advanced graduate students from diverse biological fields. Topics to be covered include but are not limited to acquisition and organization of next generation sequence data; principles of quality control of sequence data and data management; methods of taxonomic assignment and clustering of targeted gene data; assembly, functional classification and characterization of shotgun metagenomic data; statistical models for estimating microbial diversity; and microbial community comparison methodology and metrics. The workshop also includes an introduction to the Linux command-line and R statistical environments. 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. Guided by authors of resources including CatchAll, LEfSe, mothur, Oligotyping, MetaPathways, MetaPhlAn, PhyloSeq, QIIME, USEARCH, Unifrac, and VAMPS, participants in the workshop will have the opportunity to compare different analysis techniques for molecular data, analyze their own data, and discuss their data and analyses with faculty.

Financial Information: Tuition: $2,200.00. Room & Board: $770.00. Some limited financial assistance may be available.

2019 Course Faculty

Mihai Pop, University of Maryland
Tracy Teal, The Carpentries
Yana Bromberg, Yale University
Titus Brown, University of California Davis
Ben Callahan, North Carolina State University
Susan Holmes, Stanford University
Adina Howe, Iowa State University
Rob Knight, University of California San Diego
Mike Lee, NASA Ames Research Center
Christian Müller, Simons Foundation
Todd Treangen, Rice University
Tandy Warnow, University of Illinois at Urbana–Champaign
Amy Willis, University of Washington