q2-confluence tutorial
README · Installation · Tutorial · Data preparation
⚠️ This tutorial and the rachis plugins it uses are in early testing (alpha release) phase. Commands will almost certainly change. Be skeptical of any surprising results - testing is still in progress.
The tutorial integrates 16S rRNA amplicon and metagenome profiles of the same samples in the feature space of one GTDB release’s genomes, with the q2-confluence and mosh-sylph plugins for QIIME 2.
Start by installing. Then work through the tutorial. A separate page describes how the tutorial data were prepared with QIIME 2 (Bolyen et al. (2019)) (for amplicon data) and MOSHPIT (Ziemski et al. (2026)) (for metagenome data).
The tutorial is published at gregcaporaso.github.io/q2-confluence-tutorial, and its source is at github.com/gregcaporaso/q2-confluence-tutorial.
Questions and bug reports should be directed to the QIIME 2 Forum.
AI disclosure
The first draft of this tutorial’s commands and text were written by Claude Code, orchestrated by @gregcaporaso.
@gregcaporaso tested every command by hand and is writing the text based on an initial outline by Claude Code.
The commit history describes what was requested and what the assistant implemented.
AI disclosures for the new plugins developed for this tutorial are available in their respective README files: the mosh-sylph README and the q2-confluence README.
As of this writing (2 November 2026) the text is a work in progress.