Drinking from a fire hose: analysis of metagenomic data Rachel Mackelprang, Ph.D. Assistant Professor of Biology California State University Northridge.

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Presentation transcript:

Drinking from a fire hose: analysis of metagenomic data Rachel Mackelprang, Ph.D. Assistant Professor of Biology California State University Northridge Ph.D. Comics

(Alas) There is no one pipeline There’s more than one way to do it -Larry Wall Questions and goals Community complexity & diversity Computational resources and expertise

Goals & Questions The breadth vs depth conundrum Genomes/large conitgs? Hess et al Compare ecological patterns with genetic content? Tas et al Gene & pathway abundance? Mason et al. 2012

Computational Resources & Requirements Environment 1 Environment 2 Gene 1 Gene 2 Gene 3 Gene 1 Gene 2 Gene 3 Assembly Direct Annotation of Reads Large memory requirements Freely Available Tools Velvet ABySS Meta-IDBA ALLPATHS khmer Loads of nodes Freely Available Tools BLAST USEARCH PAUDA HMMER3

Community Characteristics © Christian Lott Diversity 0.5 Tb per sample isn’t nearly enough Sanger sequencing yielded reasonable coverage

Thank you Looking forward to an interesting discussion