Introduction 🥾
q2-boots is a QIIME 2 plugin providing bootstrapped and rarefaction-based (collectively, resampled) alpha and beta diversity analyses, designed to mirror the interface of q2-diversity.
Development status
q2-boots is in beta release. It is sufficiently validated and ready for real-world data analysis, but interfaces are still subject to change. For example, default parameter settings, command names, and outputs generated by specific commands may evolve as we get usability feedback and feature requests from users.
Are you in the right place?
This is the q2-boots Documentation, which is plugin-specific documentation. If you’re looking to get started with QIIME 2, or for general information about the project, there are better resources.
Are you looking for:
- the QIIME 2 homepage? That’s https://qiime2.org.
- learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
- learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
- installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
- general help? See the QIIME 2 Forum
- information about the author? See https://cap-lab.bio.
Otherwise, if you’re specifically looking for the q2-boots Documentation, you’re in the right place. Read on... 📖
Installing¶
To install q2-boots, refer to the installation instructions on the q2-boots Library page.
Using¶
After installing q2-boots, you can read the Gut-to-soil axis tutorial 💩🌱 to see how it’s integrated in a microbiome analysis.
For a full list of the actions that can be performed with q2-boots, including usage examples that you can run on your own, refer to the plugin reference.
Citing¶
If you use q2-boots in any published work, please cite Raspet et al. (2025).
License¶
q2-boots Documentation (©2025) by Caporaso Lab is licensed under CC BY-NC-ND 4.0.
- Raspet, I., Gehret, E., Herman, C., Meilander, J., Manley, A., Simard, A., Bolyen, E., & Caporaso, J. G. (2025). Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots. F1000Res., 14(87), 87. https://doi.org/10.12688/f1000research.156295.1