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Users
This section is for people who run analyses with MetaManifold: from raw paired-end FASTQs to filtered, taxonomy-annotated tables and interactive figures. You do not need to be a programmer. You do need sequencing data.
Two audiences share this section, and they want different things from the same software:
- Academics — you are answering a research question and will publish. You care about reproducibility, method disclosure, exactness of what is claimed, and citing the software. Your home is For Academics, but read the install and first-study pages first like everyone else.
- Lab professionals — you are running samples as a service: routine panels, QC gates before results leave the lab, primer and database management, contamination curation. Your home is For Lab Professionals.
Where guidance differs, pages carry Academics: and Lab professionals: callouts. Where it does not, they just tell you how the thing works.
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Install and First Run — prerequisites,
install.sh, starting the server. (~20 minutes including downloads.) - Your First Study — put FASTQs where they belong, launch a run, find your tables. (~15 minutes plus compute time.)
- Exploring Results — QC, the results explorer, annotation and composition views.
- Analysis and Statistics Today — what each analysis computes, and what it refuses to compute.
- Your track: For Academics or For Lab Professionals.
- Configuration Reference — the full YAML reference, when you need the exact key.
- Troubleshooting — when something refuses.
IN PLACE today: the full pipeline (both ASV and OTU lanes), the browser workbench (config editors, runs and jobs, QC, results explorer, annotation and curation, composition), and the analysis surface: alpha diversity with honest significance statuses, composition bars, organism categories, taxon overlap, NMDS and PERMANOVA, exact descriptive summaries, ML fits (NB-GLM / CLR-ILR linear models / logistic) with refusal states, and exact TSS/CSS/RSS offsets.
COMING (tracked, not yet available to you): exact statistical tests (#3),
compositional differential-abundance methods (#5), occupancy models (#17),
constrained ordinations (#18→#19), PhILR/SBP balances (#20), advanced zero
handling (#21), CladeCumulus (#6), Full Evidence Mode (#7), Zenodo DOI
minting (#8), standalone offline installers and the coordinated updater
(docs/migration/STATUS.md). The full board:
Status and Roadmap.
A promise the software keeps: when it cannot compute something validly, it says so and returns an unsuccessful state — never a plausible-looking number. Refusals are a feature. See Analysis and Statistics Today.