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

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Supplemental Information

Supplementary File 1 contains the QIIME 2 .qzv files corresponding to Figure 1a-d

These are also accessible at https://github.com/qiime2/paper1 and can be viewed using QIIME 2 View ( https://view.qiime2.org ) where readers can interact with the results, and explore the methods used to generate them (see the Provenance tab after loading a .qzv file with QIIME 2 View).

DOI: 10.7287/peerj.preprints.27295v1/supp-1

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Evan Bolyen conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, design of QIIME 2 framework, development of documentation/educational/support content.

Jai Ram Rideout conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, design of QIIME 2 framework, development of documentation/educational/support content.

Matthew R Dillon conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, design of QIIME 2 framework, development of documentation/educational/support content.

Nicholas A Bokulich conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, design of QIIME 2 framework, development of documentation/educational/support content.

Christian Abnet approved the final draft, provided early test data, advising on visualization approaches.

Gabriel A Al-Ghalith contributed reagents/materials/analysis tools, approved the final draft.

Harriet Alexander contributed reagents/materials/analysis tools, approved the final draft.

Eric J Alm contributed reagents/materials/analysis tools, approved the final draft.

Manimozhiyan Arumugam contributed reagents/materials/analysis tools, approved the final draft.

Francesco Asnicar contributed reagents/materials/analysis tools, approved the final draft.

Yang Bai approved the final draft, developed Chinese translation of user documentation.

Jordan E Bisanz approved the final draft, provided user documentation illustrating how to analyze QIIME 2 results in R.

Kyle Bittinger contributed reagents/materials/analysis tools, approved the final draft.

Asker Brejnrod contributed reagents/materials/analysis tools, approved the final draft.

Colin J Brislawn approved the final draft, provided extensive technical support to users.

C Titus Brown approved the final draft, advised on the development of q2-sourmash plugin.

Benjamin J Callahan contributed reagents/materials/analysis tools, approved the final draft.

Andrés Mauricio Caraballo-Rodríguez approved the final draft, developed documentation for q2-metabolomics plugin.

John Chase contributed reagents/materials/analysis tools, approved the final draft.

Emily Cope approved the final draft, provided feedback integral to the development of QIIME 2 methods/visualizations/workflows; assisted with teaching of QIIME 2.

Ricardo Da Silva approved the final draft, developed documentation for q2-metabolomics plugin.

Pieter C Dorrestein approved the final draft, coordinated the development of multiple QIIME 2 metabolomics plugins.

Gavin M Douglas contributed reagents/materials/analysis tools, approved the final draft.

Daniel M Durall approved the final draft, developed and disseminated ITS-based taxonomy classifiers.

Claire Duvallet contributed reagents/materials/analysis tools, approved the final draft.

Christian F Edwardson approved the final draft, developed documentation illustrating how to use QIIME 2 data with phyloseq.

Madeleine Ernst contributed reagents/materials/analysis tools, approved the final draft.

Mehrbod Estaki approved the final draft, provided extensive technical support to users.

Jennifer Fouquier contributed reagents/materials/analysis tools, approved the final draft.

Julia M Gauglitz approved the final draft, developed documentation for q2-metabolomics plugin.

Deanna L Gibson approved the final draft, advised other contributors to QIIME 2, and coordinated and hosted a QIIME 2 workshop.

Antonio Gonzalez contributed reagents/materials/analysis tools, approved the final draft.

Kestrel Gorlick contributed reagents/materials/analysis tools, approved the final draft.

Jiarong Guo contributed reagents/materials/analysis tools, approved the final draft.

Benjamin Hillmann contributed reagents/materials/analysis tools, approved the final draft.

Susan Holmes approved the final draft, advised on the development of q2-dada2 plugin.

Hannes Holste contributed reagents/materials/analysis tools, approved the final draft.

Curtis Huttenhower contributed reagents/materials/analysis tools, approved the final draft.

Gavin Huttley contributed reagents/materials/analysis tools, approved the final draft.

Stefan Janssen contributed reagents/materials/analysis tools, approved the final draft.

Alan K Jarmusch approved the final draft, developed documentation for q2-metabolomics plugin.

Lingjing Jiang contributed reagents/materials/analysis tools, approved the final draft.

Benjamin Kaehler contributed reagents/materials/analysis tools, approved the final draft.

Kyo Bin Kang approved the final draft, developed documentation for q2-metabolomics plugin.

Christopher R Keefe contributed reagents/materials/analysis tools, approved the final draft.

Paul Keim approved the final draft, advised other contributors and provided feedback integral to the development of QIIME 2 methods/visualizations/workflows.

Scott T Kelley approved the final draft, developed educational content for QIIME 2.

Dan Knights contributed reagents/materials/analysis tools, approved the final draft.

Irina Koester approved the final draft, developed documentation for q2-metabolomics plugin.

Tomasz Kosciolek approved the final draft, developed documentation for the QIIME 2 artifact API.

Jorden Kreps contributed reagents/materials/analysis tools, approved the final draft.

Morgan GI Langille contributed reagents/materials/analysis tools, approved the final draft.

Joslynn Lee approved the final draft, developed educational content for QIIME 2.

Ruth Ley approved the final draft, advised other contributors.

Yong-Xin Liu approved the final draft, developed Chinese translation of user documentation.

Erikka Loftfield approved the final draft, provided early test data, advising on visualization approaches.

Catherine Lozupone contributed reagents/materials/analysis tools, approved the final draft.

Massoud Maher contributed reagents/materials/analysis tools, approved the final draft.

Clarisse Marotz contributed reagents/materials/analysis tools, approved the final draft.

Bryan D Martin contributed reagents/materials/analysis tools, approved the final draft.

Daniel McDonald contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.

Lauren J McIver contributed reagents/materials/analysis tools, approved the final draft.

Alexey V Melnik approved the final draft, developed documentation for q2-metabolomics plugin.

Jessica L Metcalf approved the final draft, provided feedback integral to the development of QIIME 2 methods/visualizations/workflows; assisted with teaching of QIIME 2; developed QIIME 2 educational content.

Sydney C Morgan approved the final draft, developed and disseminated ITS-based taxonomy classifiers.

Jamie Morton contributed reagents/materials/analysis tools, approved the final draft.

Ahmad Turan Naimey contributed reagents/materials/analysis tools, approved the final draft.

Jose A Navas-Molina contributed reagents/materials/analysis tools, approved the final draft.

Louis Felix Nothias approved the final draft, developed documentation for q2-metabolomics plugin.

Stephanie B Orchanian approved the final draft, developed documentation for QIIME 2.

Talima Pearson approved the final draft, provided feedback integral to the development of QIIME 2 methods/visualizations/workflows.

Samuel L Peoples contributed reagents/materials/analysis tools, approved the final draft.

Daniel Petras approved the final draft, developed documentation for q2-metabolomics plugin.

Mary Lai Preuss contributed reagents/materials/analysis tools, approved the final draft.

Elmar Pruesse contributed reagents/materials/analysis tools, approved the final draft.

Lasse Buur Rasmussen contributed reagents/materials/analysis tools, approved the final draft.

Adam Rivers contributed reagents/materials/analysis tools, approved the final draft.

Michael S Robeson, II contributed reagents/materials/analysis tools, approved the final draft.

Patrick Rosenthal contributed reagents/materials/analysis tools, approved the final draft.

Nicola Segata contributed reagents/materials/analysis tools, approved the final draft.

Michael Shaffer contributed reagents/materials/analysis tools, approved the final draft.

Arron Shiffer approved the final draft, developed educational content for QIIME 2; taught QIIME 2.

Rashmi Sinha approved the final draft, provided early test data, advising on visualization approaches.

Se Jin Song approved the final draft, provided feedback integral to the development of QIIME 2 methods/visualizations/workflows; developed educational content for QIIME 2; taught QIIME 2.

John R Spear approved the final draft, collaborated on the collection of Yellowstone (Figure 1c) data.

Austin D Swafford approved the final draft, developed documentation for QIIME 2.

Luke R Thompson approved the final draft, developed documentation for QIIME 2.

Pedro J Torres approved the final draft, provided early feedback on QIIME 2 that frequently led to upgrades and/or bug fixes.

Pauline Trinh contributed reagents/materials/analysis tools, approved the final draft.

Anupriya Tripathi contributed reagents/materials/analysis tools, approved the final draft.

Peter J Turnbaugh approved the final draft, advised other contributors.

Sabah Ul-Hasan approved the final draft, developed documentation for q2-metabolomics plugin.

Justin JJ van der Hooft contributed reagents/materials/analysis tools, approved the final draft.

Fernando Vargas approved the final draft, developed documentation for q2-metabolomics plugin.

Yoshiki Vázquez-Baeza contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.

Emily Vogtmann approved the final draft, provided early test data, advising on visualization approaches.

Max von Hippel contributed reagents/materials/analysis tools, approved the final draft.

William Walters approved the final draft, developed and disseminated Silva-based taxonomy classifiers.

Yunhu Wan approved the final draft, provided early feedback on QIIME 2 that frequently led to upgrades and/or bug fixes.

Mingxun Wang contributed reagents/materials/analysis tools, approved the final draft.

Jonathan Warren approved the final draft, developed documentation for QIIME 2.

Kyle C Weber contributed reagents/materials/analysis tools, approved the final draft.

Chase HD Williamson approved the final draft, collaborated on the collection of Yellowstone (Figure 1c) data.

Amy D Willis contributed reagents/materials/analysis tools, approved the final draft.

Zhenjiang Zech Xu contributed reagents/materials/analysis tools, approved the final draft.

Jesse R Zaneveld contributed reagents/materials/analysis tools, approved the final draft.

Yilong Zhang contributed reagents/materials/analysis tools, approved the final draft.

Rob Knight conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

J Gregory Caporaso conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Yellowstone Center for Resources provided research permit #5664 to JRS for Yellowstone access and sample collection (Figure 1c).

Data Deposition

The following information was supplied regarding data availability:

QIIME 2 is open source and free for all use, including commercial. It is licensed under the BSD 3-clause license. Source code is available at https://github.com/qiime2.

Data for the analyses presented in Figure 1 are available as follows: (a) Earth Microbiome Project data was obtained from ftp://ftp.microbio.me/emp/release1, and the American Gut Project (AGP) data was obtained from Qiita (http://qiita.microbio.me) study 10317. (b) Sequence data are available in Qiita under study id 10249 and EBI under accession number ERP016173. (c) Sequence data are available in Qiita under study id 925 and EBI under accession number ERP022167. (d) Data are available in the q2-ili GitHub repository (https://github.com/biocore/q2-ili). Interactive versions of the Figure 1 visualizations can be accessed at https://github.com/qiime2/paper1.

Funding

QIIME 2 development was primarily funded by NSF Award 1565100 to JGC and RK. Partial support was also provided from the following grants: NIH U54CA143925 (JGC, TP) and U54MD012388 (JGC, TP); grants from the Alfred P. Sloan Foundation (JGC, RK); ERC-STG project MetaPG (NS); Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (YB); from the Australian National Health and Medical Research Council APP1085372 (GAH, JGC, Von Bing Yap and RK); and from Natural Sciences and Engineering Research Council (NSERC) to DLG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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