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MetaManifold

Amplicon metabarcoding from raw paired-end Illumina reads to filtered, taxonomy-annotated ASV/OTU tables — one Julia engine, one browser workbench, and statistics that say what they cannot claim.

This wiki is the long-form documentation for MetaManifold-WebUI (origin design by Joshua Jewell; maintained and extended on the hyperpolymath fork). It is written in the berrywiki page format: plain Markdown with hidden tree metadata, so it survives with nothing but git and a browser.

Three doors — pick the one that is yours

If you are…	Start here	What you get
A user — running analyses (academic or lab professional)	Users	Install, your first study, the configuration reference, the analysis surface — with separate tracks for academics (reproducibility, citing, exactness) and lab professionals (routine throughput, QC, curation).
A platform maintainer — running the platform or the repository	Maintainers	Operator track (deployment, databases, toolchains, upgrades) and steward track (CI gates, reviews, upstream relations, estate compliance).
A developer — changing the code	Developers	Architecture tour, the type system, statistics internals, extension points, tests and the REST surface.

Beyond the three doors, two cross-cutting sections:

• Deep Dives — the mathematics and engineering receipts that the README and EXPLAINME deliberately keep short: the three-layer design progression, type theory meets statistics, exact arithmetic, maximum likelihood and refusals, compositional statistics and offsets, epistemic status, and the advanced functionality that is coming.
• Status and Roadmap — the single board that marks, for every area, what is here now and what is coming.

Status legend — used on every page

Every section that could be mistaken for a promise carries one of four markers. They are used strictly:

• IN PLACE — implemented and verifiable in the tree today.
• PARTIAL — usable now, with the limits named on the spot.
• COMING — specified and tracked (issue numbers given), not implemented. Never listed as a feature of the present.
• BLOCKED — deliberately halted pending a named condition.

If a claim has no marker, it is a description of what the software does today. When in doubt, the Status and Roadmap board is authoritative, and the repository tree is the final arbiter.

Orientation in ninety seconds

MetaManifold is three designs stacked on each other (full story in Deep Dives — Design Progression):

1. The base design (R/Python): raw DADA2 (R) for ASVs and the swarm/vsearch shell tradition for OTUs — the science, used as published.
2. The MetaManifold augmentation (JoshuaJewell): a Julia orchestrator that runs both lanes per run and a web workbench (config cascade, QC, results, annotation, composition) over a per-run DuckDB store.
3. The hyperpolymath steps (this fork): honest statistics (real maximum-likelihood fits or explicit refusals; exact counts and rationals; exact TSS/CSS/RSS offsets), a typed frontend estate, and CI/tests/ benchmarks that keep every claim checkable.

Conventions

• Academics vs lab professionals. Where the two audiences need different guidance, pages carry Academics: and Lab professionals: callouts; where the guidance is shared, nothing is split.
• Issue references use #n for this repository's tracker. Upstream references are named in full (e.g. JoshuaJewell/MetaManifold-WebUI).
• Source of truth. These pages are sourced from docs/wikis/ in the repository and published here; see docs/wikis/README.md for the sync convention.