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Sagun Maharjan edited this page Sep 27, 2023 · 28 revisions

bioBakery tools for meta'omic profiling

Welcome to the bioBakery tools and tutorials wiki, which provides software, documentation, and tutorials for methods for microbial community profiling developed by the Huttenhower lab. Most tools are supported both as individual software packages (typically Python or R) and within the bioBakery virtual image, a pre-built platform that provides meta'omic analysis tools already installed with dependencies and configuration. For the integrated bioBakery virtual environment, please click on the button below for more information:


If you use bioBakery in your work, please cite the paper:

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018 Apr 1;34(7):1235-1237. PMID: 29194469

Microbial community profiling

This set of methods generally provide reference-based profiles of microbial community features, e.g. taxonomic abundances (MetaPhlAn) or functional profiles (genes and/or pathways, HUMAnN). They apply broadly to sequence-based data (metagenomes and metatranscriptomes), with some methods applying to other types of culture-independent molecular data. Please click individual links for detailed tutorials:

HUMAnN2 MetaPhlAn PhyloPhlAn PICRUSt ShortBRED PPANINI StrainPhlAn MelonnPan WAAFLE.png MetaWIBELE.png macarron.png FUGAsseM.png

Downstream analysis and statistics

The methods in this section generally provide quantitative models for interpreting microbial community profiles as generated by the methods above. For example, this includes identifying significant associations of sample metadata (phenotype, environment, health status, etc.) with microbial taxonomic or functional composition. Please click on the links below for detailed tutorials:


Infrastructure and utilities

GraPhlAn KneadData AnADAMA workflows


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