Clone wiki

biobakery / Home

Huttenhower Lab Tools

Welcome to the lab tools and tutorials wiki. Most tools are now supported through the bioBakery, a virtual environment platform that provides meta'omic analysis tools (already installed with dependencies and configuration!) Please click on the button below for more information:

https://bitbucket.org/repo/49y6o9/images/2814622477-biobakery_logo.png

The wiki also provides tutorials for individual lab tools, providing links to source code and downloads and illustrating through demonstration data how to use these for your own research.

Composition Analysis

These tools can determine microbial community composition in terms of (i) microbial taxa and their associated abundances (e.g. MetaPhlAn) or (ii) genes and associated pathways (e.g. HUMAnN) in a metagenome or metatranscriptome. Please click on the links below for detailed tutorials:

HUMAnN2 MetaPhlAn PhyloPhlAn PICRUSt ShortBRED PPANINI StrainPhlAn MelonnPan

Statistical Analysis

These tools provide various quantitative models for interpreting processes microbial community data. For example, this includes identifying significant associations of sample metadata (phenotype, environment, etc.) with microbial taxonomic or functional composition. Please click on the links below for detailed tutorials:

HAllA ARepA CCREPE LEfSe MaAsLin microPITA SparseDOSSA BAN

Infrastructure and Utilities

GraPhlAn KneadData AnADAMA workflows

Notes

Updated