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biobakery

Tools Shell

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:

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

Notes



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