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

Non-human synthetic metagenomes and gold standards used for the evaluation of MetaPhlAn and HUMAnN 3:

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 papers:

Francesco Beghini1 Lauren J McIver2 Aitor Blanco-Mìguez1 Leonard Dubois1 Francesco Asnicar1 Sagun Maharjan2,3 Ana Mailyan2,3 Andrew Maltez Thomas1 Paolo Manghi1 Matthias Scholz2,3 Mireia Valles-Colomer1 George Weingart2,3 Yancong Zhang2,3 Moreno Zolfo1 Curtis Huttenhower2,3 Eric A Franzosa2,3 Nicola Segata1,5

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3


1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, Italy

5 IEO, European Institute of Oncology IRCCS, Milan, Italy

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 (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