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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #359550
Research Project: Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

Title: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Author
item BOLYEN, EVAN - Northern Arizona University
item RIDEOUT, JAI RAM - Northern Arizona University
item DILLON, MATTHEW - Northern Arizona University
item BOKULICH, NICHOLAS - Northern Arizona University
item ABNET, CHRISTIAN - National Cancer Institute (NCI, NIH)
item AL-GHALITH, GABRIEL - University Of Minnesota
item ALEXANDER, HARRIET - Woods Hole Oceanographic Institute (WHOI)
item ALM, ERIC - Massachusetts Institute Of Technology
item ARUMUGAM, MANIMOZHIYAN - University Of Copenhagen
item ASNICAR, FRANCESCO - University Of Trento, Italy
item Rivers, Adam

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2019
Publication Date: 7/24/2019
Citation: Bolyen, E., Rideout, J., Dillon, M., Bokulich, N., Abnet, C., Al-Ghalith, G., Alexander, H., Alm, E., Arumugam, M., Asnicar, F., Rivers, A.R. 2019. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0209-9.
DOI: https://doi.org/10.1038/s41587-019-0209-9

Interpretive Summary: We present QIIME 2, free software to enable scientists, engineers, clinicians and policy makers to analyze microbial communities and microbiomes. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for a wide range of scientific data types including DNA and chemical data, and robust tracking systems to document how scientific results are produced.

Technical Abstract: We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.