bioBakery: a meta'omic analysis environment.
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| 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 () 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. |
| Year of Publication | 2018
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| Journal | Bioinformatics
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| Volume | 34
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| Issue | 7
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| Pages | 1235-1237
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| Date Published | 2018 04 01
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| ISSN | 1367-4811
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| DOI | 10.1093/bioinformatics/btx754
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| PubMed ID | 29194469
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| PubMed Central ID | PMC6030947
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| Grant list | R01 HG005220 / HG / NHGRI NIH HHS / United States
R01 HG005969 / HG / NHGRI NIH HHS / United States
U54 DE023798 / DE / NIDCR NIH HHS / United States
U54 DK102557 / DK / NIDDK NIH HHS / United States
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