QIIME 2 Cancer AutoFMT Tutorial

The QIIME 2 Cancer AutoFMT Tutorial Jupyter Book (q2-cat-book) was originally developed for the 2024 ITN / QIIME 2 Workshop, taught 27 - 29 August 2024 at the National Institutes of Health.

Code of Conduct

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 as you become involved in the QIIME 2 community.

Relevant links and protocols

• QIIME 2 Forum: Technical support and many other resources.

• Project homepage: Announcements and other relevant links.

• YouTube channel: Full video courses in videos ranging from 5-60 minutes.

• User Documentation: The official QIIME 2 user documentation. This is in the process of being refactored and will transition to a new URL shortly.

• Developing with QIIME 2: A free online book for bioinformatics software developers looking to make their tools accessible in the QIIME 2 ecosystem. Includes a step-by-step guide to building your first QIIME 2 plugin.

• Linkedin: A new LinkedIn group for the QIIME 2 community.

Recommended readings

The following readings will provide background information for this tutorial. These are presented in priority order.

1. Assessing Engraftment Following Fecal Microbiota Transplant (Herman et al. [HBB+24])

2. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant (Taur et al. [TCS+18])

3. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients (Liao et al. [LTC+21])

4. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Bolyen et al. [BRD+19])

5. q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data (Bokulich et al. [BDZ+18])

6. Getting started with QIIME 2

7. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops (Dillon et al. [DBA+21])

Your instruction team

Name	Affiliation(s)
J. Gregory Caporaso	Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA
Johannah Hagen	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
Colin Wood	Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA
Colin Brislawn	Independent Scientist, USA
Carrie Wright	Fred Hutch Cancer Center, USA
Candace Savonen	Fred Hutch Cancer Center, USA
Kate Isaac	Fred Hutch Cancer Center, USA

We additionally thank the many instructors who were involved in preparing the content used in this tutorial, including preparing the data and the written and video tutorials for the Cancer Microbiome Intervention Tutorial from which this content is derived.

Thank you to our funders

This workshop was funded in part by NIH National Cancer Institute Informatics Technology for Cancer Research grant 1U24CA248454-01 to JGC and UE5CA254170 to the ITCR Training Network.

QIIME 2 is additionally funded by 1U24CA248454-01, and grants from the Chan Zuckerberg Initiative (CZI) DAF, an advised fund of Silicon Valley Community Foundation, to JGC including DAF2019-207342 (CZI grant DOI: 10.37921/862772dbrrej; funder DOI 10.13039/100014989). Initial support for the development of QIIME 2 was provided through a grant from the National Science Foundation to JGC.

The Cancer Galaxy server used in this event is funded in part by NIH grants U24CA231877 and U24HG006620 to Jeremy Goecks.

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.

This website is built with MyST Markdown and Jupyter Book, which are supported in part with funding from the Alfred P. Sloan Foundation.

Reusing

q2-cat-book by Caporaso Lab is licensed under CC BY-NC-SA 4.0.

You are free distribute, remix, adapt, and build upon the material in any medium or format, for noncommercial purposes only, as long as credit is given to the original creator. Adaptations must be shared under the same terms.