OncoTracer

OncoTracer analyzes Illumina and Oxford Nanopore reads for DNA copy-number changes and optional small variants. Configure samples, choose Fresh or FFPE preservation, and review results through its browser interface. For research use.

Install

OncoTracer supports 64-bit Linux and Python 3.10–3.13. Install the command in your Python environment:

pip install oncotracer

No Git checkout is required. Pip installs the application and its bundled workflow resources. Choose one backend to prepare and verify the scientific tools before analysis.

With Conda available:

oncotracer install --conda
oncotracer --interactive --backend conda

With Docker running and accessible:

oncotracer install --docker
oncotracer --interactive --backend docker

Choose the sequencing platform and Fresh or FFPE inside the browser, then select inputs, settings and a project folder. Save and check before choosing Run. Optional callers, models and licensed annotation resources are configured separately.

For concurrent analyses, open another terminal and use a different project/output folder. Sessions select available browser ports; allocate CPU and memory for each run.

Uninstall

To remove an additional global launcher while keeping scientific tools and projects:

oncotracer uninstall --global-launcher --yes
python -m pip uninstall oncotracer

Use the Python environment where you installed the package for the pip command. To remove managed scientific tools too, first preview oncotracer uninstall --conda --dry-run and then use oncotracer uninstall --conda --yes.

Documentation

• Installation and backend requirements
• Browser setup
• Variants and FFPE resources
• Nextflow entry point
• Source and issues