bioBakery tools for meta'omic profiling

bioBakery is a suite of software, tutorials, and workflows of methods developed by the Huttenhower lab and the Segata lab for performing analyses on microbial communities from metagenomic data.

The following tools developed by the Segata Lab are included in bioBakery:

Software repository and supporting material

Software repository of bioBakery:

The bioBakery manual:

User support (email-based group and discussion forum):


If you find this tool useful in your research, please cite our paper:

Lauren J McIver1,2 Galeb Abu-Ali1,2 Eric A Franzosa1,2 Randall Schwager1,2 Xochitl C Morgan1,2,3 Levi Waldron4 Nicola Segata5 Curtis Huttenhower1,2

bioBakery: a meta'omic analysis environment

Bioinformatics in press (2018) 10.1093/bioinformatics/btx754

1 Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

2 The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

3 Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand.

4 Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA.

5 Centre for Integrative Biology, University of Trento, Trento, Italy