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. 2018 Apr 1;34(7):1235-1237.
doi: 10.1093/bioinformatics/btx754.

bioBakery: a meta'omic analysis environment

Lauren J McIver  1   2 , Galeb Abu-Ali  1   2 , Eric A Franzosa  1   2 , Randall Schwager  1   2 , Xochitl C Morgan  1   2   3 , Levi Waldron  4 , Nicola Segata  5 , Curtis Huttenhower  1   2
Affiliations

bioBakery: a meta'omic analysis environment

Lauren J McIver et al. Bioinformatics. .

Abstract

Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.

Availability and implementation: bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.

Contact: chuttenh@hsph.harvard.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
The default metagenome workflow incorporates several individual tools that together process raw sequences into a set of data products, reports and visualizations
See this image and copyright information in PMC

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