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ont-ecosystem

The Athey Lab's Oxford Nanopore analysis framework. Unified library, CLI, and skill catalog for ONT + PacBio long-read workflows — from basecalling and alignment through targeted-enrichment QC, pharmacogenomic genotyping, and publication-quality figure generation.

114skills
89CLI tools
155library modules
GitHub repo Quick start Skills catalog

Getting started

Installation

Clone the repo, install dependencies, run the bootstrap script.

INSTALLATION.md →

Quick start

Common workflows: list experiments, run the SMA-seq pipeline, sync the registry.

QUICKSTART.md →

CLI reference

All 89 command-line tools, their flags, and when to reach for each.

CLI_REFERENCE.md →

Skill catalog

Analysis skills

/fast-subsample, /sma-pipeline, /ont-align, /cas9-enrichment, /pypgx, /aldy, /end-reason, /comprehensive-analysis …

Full catalog →

Manuscript & wiki

/lab-manuscript, /lab-submission-check, /lab-paper-status, /lab-refs, /lab-wiki, /lab-query, /lab-transcripts.

Skill reference →

Registry & operations

/experiment-db, /ont-explorer, /registry-validator, /health-check, /consolidate, /skill-doctor, /plugin-doctor.

REGISTRY.md →

Reference docs

Architecture

SSOT rule, skill layout, bin wrappers, registry flow.

ARCHITECTURE.md →

System architecture

End-to-end layout of the framework.

SYSTEM_ARCHITECTURE.md →

API reference

lib/ module surface.

API_REFERENCE.md →

Module index

All 155 library modules.

MODULE_INDEX.md →

Development

Testing, linting, contribution flow.

DEVELOPMENT.md →

GitHub integration

Registry sync, auto-commit patterns.

GITHUB.md →

Related work in the ecosystem

Athey Lab hub

Cross-paper + cross-project landing page.

fragment-viewer

CE/GeneMapper fragment analyzer (public).

Lab website

Public-facing lab homepage.

lab-wiki

Decisions, meetings, entities (private).