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- Title
BioBakery: a meta'omic analysis environment.
- Authors
McIver, Lauren J; Abu-Ali, Galeb; Franzosa, Eric A; Schwager, Randall; Morgan, Xochitl C; Waldron, Levi; Segata, Nicola; Huttenhower, Curtis
- Abstract
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 preconfigured 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.
- Subjects
APPLICATION software research; VIRTUAL machine systems; SOFTWARE sequencers; MICROBIAL communities; QUANTITATIVE research
- Publication
Bioinformatics, 2018, Vol 34, Issue 7, p1235
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btx754