Community-led, integrated, reproducible multi-omics with anvi’o

Type Article
Date 2021-01
Language English
Author(s) Eren A. MuratORCID1, 2, 3, 4, Kiefl EvanORCID1, 4, Shaiber AlonORCID1, 4, Veseli IvaORCID1, 4, Miller Samuel E.1, Schechter Matthew S.ORCID1, 2, Fink IsaacORCID1, Pan Jessica N.ORCID1, Yousef Mahmoud1, Fogarty Emily C.ORCID1, 2, Trigodet FlorianORCID1, Watson Andrea R.1, 2, Esen Özcan C.1, Moore Ryan M.ORCID4, Clayssen QuentinORCID5, Lee Michael D.ORCID6, 7, Kivenson VeronikaORCID8, Graham Elaina D.ORCID9, Merrill Bryan D.ORCID10, Karkman AnttiORCID11, Blankenberg DanielORCID12, 13, Eppley John M.ORCID14, Sjödin AndreasORCID15, Scott Jarrod J.16, Vázquez-Campos XabierORCID17, McKay Luke J.18, 19, McDaniel Elizabeth A.ORCID20, Stevens Sarah L. R.21, 22, Anderson Rika E.23, Fuessel Jessika1, 24, Fernandez-Guerra Antonio25, Maignien Lois2, 26, Delmont Tom O.27, Willis Amy D.ORCID28
Affiliation(s) 1 : Department of Medicine, University of Chicago, Chicago, IL, USA
2 : Committee on Microbiology, University of Chicago, Chicago, IL, USA
3 : Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
4 : Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
5 : Center for Bioinformatics and Computational Biology, University of Delaware, Delaware, DE, USA
6 : Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
7 : Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA
8 : Blue Marble Space Institute of Science, Seattle, WA, USA
9 : Department of Microbiology, Oregon State University, Corvallis, OR, USA
10 : Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
11 : Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
12 : Department of Microbiology, University of Helsinki, Helsinki, Finland
13 : Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
14 : Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
15 : Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai’i at Mānoa, Honolulu, HI, USA
16 : Division of CBRN Security and Defence, Swedish Defence Research Agency - FOI, Umea, Sweden
17 : Smithsonian Tropical Research Institute, Bocas del Toro, Republic of Panama
18 : NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
19 : Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
20 : Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
21 : Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA
22 : Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, USA
23 : American Family Insurance Data Science Institute, University of Wisconsin–Madison, Madison, WI, USA
24 : Department of Biology, Carleton College, Northfield, MN, USA
25 : Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
26 : Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Univ. Brest, CNRS, IFREMER, Plouzané, France
27 : Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris–Saclay, Evry, France
28 : Department of Biostatistics, University of Washington, Seattle, WA, USA
Source Nature Microbiology (2058-5276) (Springer Science and Business Media LLC), 2021-01 , Vol. 6 , N. 1 , P. 3-6
DOI 10.1038/s41564-020-00834-3
WOS© Times Cited 276
Abstract

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.

Full Text
File Pages Size Access
4 1 MB Access on demand
Author's final draft 7 678 KB Open access
Top of the page

How to cite 

Eren A. Murat, Kiefl Evan, Shaiber Alon, Veseli Iva, Miller Samuel E., Schechter Matthew S., Fink Isaac, Pan Jessica N., Yousef Mahmoud, Fogarty Emily C., Trigodet Florian, Watson Andrea R., Esen Özcan C., Moore Ryan M., Clayssen Quentin, Lee Michael D., Kivenson Veronika, Graham Elaina D., Merrill Bryan D., Karkman Antti, Blankenberg Daniel, Eppley John M., Sjödin Andreas, Scott Jarrod J., Vázquez-Campos Xabier, McKay Luke J., McDaniel Elizabeth A., Stevens Sarah L. R., Anderson Rika E., Fuessel Jessika, Fernandez-Guerra Antonio, Maignien Lois, Delmont Tom O., Willis Amy D. (2021). Community-led, integrated, reproducible multi-omics with anvi’o. Nature Microbiology, 6(1), 3-6. Publisher's official version : https://doi.org/10.1038/s41564-020-00834-3 , Open Access version : https://archimer.ifremer.fr/doc/00666/77762/