Documentation for the QIIME 2 16S rRNA amplicon pipeline
(scripts/qiime-console.py).
| I am a… | Start here | You'll get |
|---|---|---|
| PI / reviewer | PI.md | What the pipeline measures, how to read results, reproducibility & citations |
| User running it | USER.md | Step-by-step: setup → run → QC → package, with all parameters |
| Developer changing it | DEVELOPER.md | Code architecture, stage functions, extension points, gotchas |
| Maintainer operating it | MAINTAINER.md | Environment, classifier, Docker, releases, roadmap |
| Anyone needing the details | PIPELINE.md | Flow diagram + full tool/input and output tables (source of truth) |
- index.html — a single-page documentation hub (all four guides inline,
flow diagram, tool/output reference, redundancy, review deck). Open it in a browser,
or serve
docs/via GitHub Pages. Also published as a Claude Artifact.
- slides/review.md — Marp deck for a review presentation.
Pre-rendered alongside it: review.html,
review.pdf, review.pptx.
Regenerate with
marp docs/slides/review.md -o review.html(or--pdf/--pptx) ifmarp-cliis installed; the source reads fine as Markdown too.
The tables in PIPELINE.md are hand-maintained and stamped with the commit they
describe. scripts/check_docs_tables.py asserts that every qiime step and every
deliverable entry in qiime-console.py appears in those tables — run it before
merging changes that touch the pipeline.
See also the agent-oriented CLAUDE.md at the repo root.