Drinking from a fire hose: analysis of metagenomic data Rachel Mackelprang, Ph.D. Assistant...
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Transcript of Drinking from a fire hose: analysis of metagenomic data Rachel Mackelprang, Ph.D. Assistant...
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 goalsCommunity complexity & diversity
Computational resources and expertise
Goals & Questions
The breadth vs depth conundrum
Genomes/large conitgs?
Hess et al. 2011 Compare ecological patterns with genetic content?
Tas et al. 2014
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 ToolsVelvetABySS
Meta-IDBAALLPATHS
khmer
Loads of nodes
Freely Available ToolsBLAST
USEARCHPAUDA
HMMER3
Community Characteristics
© Christian Lott www.co.nrcs.usda.govwww.cnx.org
Diversity
0.5 Tb per sample isn’t nearly enough
Sanger sequencing yielded reasonable
coverage
Thank you
Looking forward to an interesting discussion