NOTICE

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SPDX-License-Identifier: CC-BY-SA-4.0
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# NOTICE — MetaManifold-WebUI

## Provenance and licensing summary

MetaManifold-WebUI as a work is **AGPL-3.0-only** (see `LICENSE`). It was
created by **Joshua Benjamin Jewell** (upstream:
`github.com/JoshuaJewell/MetaManifold-WebUI`), and this repository is the
**hyperpolymath fork** (`github.com/hyperpolymath/MetaManifold-WebUI`)
tracking that upstream.

File-level licensing follows the estate Licence Policy
(`hyperpolymath/standards`, `LICENCE-POLICY.adoc`):

| Authorship | Code / config / scripts | Prose documentation |
|---|---|---|
| Upstream files (first-committed by JoshuaJewell) | `AGPL-3.0-only` (inherited from `LICENSE`; upstream headers preserved verbatim) | `AGPL-3.0-only` |
| Fork-series files (first-committed by the hyperpolymath engineering series) | `MPL-2.0` (Rule 3a: owner-only components inside an AGPL work stay MPL-2.0) | `CC-BY-SA-4.0` |

Each source file carries an `SPDX-License-Identifier` comment stating which
row applies. Canonical licence texts: `LICENSE` (AGPL-3.0), and
`LICENSES/MPL-2.0.txt`, `LICENSES/CC-BY-SA-4.0.txt`. The authorship
classification is mechanical (first-commit author in this repository's
history) and exists to keep headers — and the CI licence check —
unambiguous; it is not a claim of copyright ownership either way.

## Third-party components

MetaManifold orchestrates, but does not vendor, third-party command-line
tools. Each is fetched from its upstream source by `install.sh` and is
subject to its own licence; no third-party binaries are included in this
repository.

| Tool | License | Source |
|---|---|---|
| [cutadapt](https://github.com/marcelm/cutadapt) | MIT | PyPI |
| [FastQC](https://github.com/s-andrews/FastQC) | GPL v3 | Babraham Bioinformatics |
| [MultiQC](https://github.com/MultiQC/MultiQC) | GPL v3 | PyPI |
| [DADA2](https://benjjneb.github.io/dada2/) | LGPL v3 | Bioconductor |
| [swarm](https://github.com/frederic-mahe/swarm) | GPL v3 | GitHub Releases |
| [vsearch](https://github.com/torognes/vsearch) | GPL v3 | GitHub Releases |
| [cd-hit](https://github.com/weizhongli/cdhit) | GPL v2+ | GitHub Releases / apt |

R/vegan and the R runtime are system components under their own licences
(GPL family). Frontend npm dependencies are declared in
`frontend/package.json` / `frontend/bun.lock` under their own licences.

## Acknowledgements and lineage

This pipeline draws on the following prior work:

- **Frédéric Mahé**: [Fred's metabarcoding pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline)
  informed the overall workflow architecture, namely the sequencing of
  primer trimming, `swarm.jl`, vsearch-based taxonomy assignment, and the
  final table merge/filter stages.
- **Benjamin J. Callahan _et al._**: [DADA2 tutorial](https://benjjneb.github.io/dada2/tutorial.html),
  used under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/), on
  which `dada2.jl` and its modules are based.

The following colleagues at the **Department of Parasitology, Charles
University** (Faculty of Science, BIOCEV, Vestec, Czech Republic)
contributed to this work:

- **Mgr. Jiří Novák** (supervisor): scripts from which several modules and
  configurations were adapted.
- **doc. Mgr. Vladimír Hampl**: provided laboratory access and resources.
- **Mgr. Paulína Pristašová**: <3.

Copyright © 2026 Joshua Benjamin Jewell (origin design) and the
hyperpolymath fork authors.

## Notices required by AGPL-3.0

This work is licensed under the GNU Affero General Public License, version
3 only (AGPL-3.0-only). As a network service, offering modified versions
requires offering the corresponding source, per AGPL §13. The canonical
source location is the repository above.