Find your way around the repository

For your first analysis

Start with the README, install OncoTracer, then use the browser setup. Run analyses in your own project folders. The source checkout supplies the software and should stay in place after an editable installation.

You do not need to edit source code or run scripts from bin/.

Which folder do I need?

Folder or file	Purpose	Who usually needs it?
README.md	Installation, uninstall and demo links	Everyone
docs/	Guides published on this documentation site	Users and contributors
examples/	Public-data manifests, checksums and example inputs	Tutorial users
params/	Advanced configuration templates	Users editing YAML manually
environments/	Conda tool specifications	Users adding optional tools
oncotracer	Launcher from the source checkout	Installation and development
oncotracer_cli/	Python application and browser interface	Developers
bin/	Analysis helpers called by OncoTracer	Developers
scripts/	Build, release and maintenance tools	Contributors
tests/	Automated validation and browser checks	Contributors
Dockerfile, docker-compose.yml	Container build and runtime definitions	Container maintainers
provenance/	Recorded software provenance	Reproducibility reviewers

Choose an example

Use QuickStart 1 first. It walks through small public Illumina and ONT inputs. QuickStart 2 covers three Illumina libraries; the full tutorial covers a larger archive.

The examples index links each dataset to its guide. Example manifests describe public or explicitly synthetic data; they are not a place to add private patient files.

Where does my work go?

Browser setup writes config/run.yml and sample tables in the project folder you select. Analysis writes results/ there, and prepared reference files are reused from the configured reference folder. Your FASTQs stay in their original location. See output files and uninstall.

For development, see the developer guide.