QIIME 2 Cancer Microbiome Intervention Tutorial

QIIME 2 Cancer Microbiome Intervention Tutorial#

This tutorial was originally developed for the 2022 NIH Foundation for Advanced Education in the Sciences Microbiome Bioinformatics with QIIME 2 workshop, taught online January 31 - February 4, 2022. It is now being publicly released with corresponding video content on the QIIME 2 YouTube channel.

This tutorial is intended to be read like a book, from beginning to end.

This tutorial and the corresponding videos present many new features of QIIME 2 and our education and documentation ecosystem, including:

  • The new QIIME 2 Galaxy-based graphical user interface;

  • New tutorial data;

  • Our new QIIME 2 documentation system, which illustrates how to use QIIME 2 with different user interfaces, including Galaxy, the QIIME 2 command line interface, the QIIME 2 Python 3 API, and the R API (via reticulate). You can choose to use whichever of these interfaces you’re most comfortable with, or use different interfaces for different steps;

  • Our first Jupyter Book-based QIIME 2 tutorial.

Important!

Please review the QIIME 2 Community Code of Conduct . All workshop instructors agreed to abide by these community expectations and we hope you will too and you become involved in the QIIME 2 community.

Thank you to our hosts and our instruction team#

We thank our hosts, the Foundation for Advanced Education in the Sciences (FAES) for their support of the initial workshop for which these materials were developed.

We thank the many instructors who were involved in preparing this content, including the data set and the written and video tutorials.

Name

Affiliation(s)

Aeriel Belk

Joint Institute for Food Safety and Applied Nutrition, United States Food and Drug Administration and the University of Maryland, USA

Nicholas A. Bokulich

Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland

Evan Bolyen

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Emily Borsom

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

J. Gregory Caporaso

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Colin J. Brislawn

Contamination Source Identification / Independent Investigator, USA

Kalen Cantrell

University of California San Diego, USA

Justine Debelius

Department of Epidemiology, Johns Hopkins School of Public Health, USA; Centre for Translational Microbiome Research, Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Sweden

Matthew Dillon

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Mehrbod Estaki

International Microbiome Centre (IMC), University of Calgary

Keegan Evans

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Marcus Fedarko

Department of Computer Science and Engineering, University of California San Diego, USA

Lena Floerl

Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland

Elizabeth Gehret

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Chloe Herman

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Ben Kaehler

School of Science, University of New South Wales, Canberra, Australia

Chris Keefe

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Lina Kim

Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland

Luca Lenzi

Centre for Genomic Research, University of Liverpool, United Kingdom

Chen Liao

Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

Huang Lin

Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), USA

Jeff Meilander

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Michael S. Robeson II, Ph.D.

Department of Biomedical Informatics, University of Arkansas for Medical Sciences, USA

Anthony Simard

Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA

Yoshiki Vazquez-Baeza

BiomeSense, USA

Thank you to our funders#

The QIIME 2 project is funded in part by:

Jupyter Book is funded by the Alfred P. Sloan to JGC Foundation.

The preparation and dissemination of the data used in this tutorial was funded in part by the National Institutes of Health (NIH) grants U01 AI124275, R01 AI137269 and U54 CA209975 to Joao B. Xavier.

QIIME 2 was initially developed with support from the National Science Foundation (1565100) to JGC.

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