Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.
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References
White, R. A., Callister, S. J., Moore, R. J., Baker, E. S. & Jansson, J. K. Nat. Protoc. 11, 2049–2053 (2016).
Callahan, A., Winnenburg, R. & Shah, N. H. Sci. Data 5, 180043 (2018).
Page, A. J. et al. Bioinformatics 31, 3691–3693 (2015).
Jalili, V. et al. Nucleic Acids Res. 48, W395–W402 (2020).
McIver, L. J. et al. Bioinformatics 34, 1235–1237 (2018).
Imelfort, M. et al. PeerJ 2, e603 (2014).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. Genome Res. 25, 1043–1055 (2015).
Arkin, A. P. et al. Nat. Biotechnol. 36, 566–569 (2018).
Eren, A. M. et al. PeerJ 3, e1319 (2015).
Tyson, G. W. et al. Nature 428, 37–43 (2004).
Werren, J. H., Baldo, L. & Clark, M. E. Nat. Rev. Microbiol. 6, 741–751 (2008).
Reveillaud, J. et al. Nat. Commun. 10, 1051 (2019).
Yeoman, C. J. et al. PeerJ 7, e7548 (2019).
Delmont, T. O. et al. eLife 8, 46497 (2019).
Köster, J. & Rahmann, S. Bioinformatics 28, 2520–2522 (2012).
Acknowledgements
The URL http://anvio.org/authors serves as a dynamic list of anvi’o developers. We thank the creators of other open-source software tools for their generosity, anvi’o users for their patience with us, and K. Lolans for her critical reading of the manuscript and suggestions. We gratefully acknowledge support for anvi’o from the Simons Foundation and Alfred P. Sloan Foundation.
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A.M.E., E.K., A. Shaiber, I.V., S.E.M., M.S.S., I.F., J.N.P., M.Y., E.C.F., F.T., A.R.W., O.C.E., R.M.M., Q.C. and A.D.W. coded and documented anvi’o, contributed to the implementation of new analytical strategies and engaged with the anvi’o community. M.D.L., V.K., E.D.G., B.D.M., A.K. and J.J.S. wrote blog posts and tutorials to make anvi’o accessible to the broader community. D.B., J.M.E., A. Sjödin, X.V.-C. and L.J.M. helped with technical issues and testing of new features on GitHub. E.A.M., S.L.R.S. and R.E.A. created undergraduate and graduate-level educational material and taught anvi’o. L.M. organized workshops for the training of research professionals. J.F., A.F.-G., L.M. and T.O.D. made intellectual contributions that influenced the direction of the platform. A.M.E. wrote the paper and prepared the figure with input from all authors.
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Eren, A.M., Kiefl, E., Shaiber, A. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 6, 3–6 (2021). https://doi.org/10.1038/s41564-020-00834-3
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DOI: https://doi.org/10.1038/s41564-020-00834-3
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