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How OncoTracer works

OncoTracer connects established analysis tools to find DNA copy-number changes (CNAs): regions with extra or missing copies of DNA. You use the oncotracer command; you do not need to run each tool yourself.

What happens to your data?

You provide sequencing files and a configuration file. OncoTracer then:

  1. Checks the input files and prepares the human reference genome.
  2. Aligns the reads to that reference.
  3. Estimates copy-number changes and refines their boundaries using the reads.
  4. Saves result tables, plots, logs, and a run summary.

The default Illumina workflow uses BWA, Picard, and qDNAseq. The default Oxford Nanopore (ONT) workflow uses minimap2, HMMcopy, and ichorCNA. See the tool list if you need the details.

What is optional?

  • Variant calling detects SNV/indel candidates from aligned reads, with platform-specific callers and Fresh/FFPE processing.

  • The optional CNA classifier adds research predictions and expanded reports. LLM-assisted report text has separate settings.

  • ONT methylation is a separate analysis. It needs modified-base BAMs or raw POD5 signal, plus additional tools and models. FASTQ files alone are not enough.

A completed run or a classifier prediction does not establish a diagnosis.

What does “native” mean?

The Python application launches the analysis tools directly. Nextflow is not required. The tools still need to be installed through a supported installation method.

Can I restart a run?

Yes. Repeat the same oncotracer run command. Completed steps are reused only when their recorded inputs, settings, and outputs still pass checks. Incomplete steps run again. See running and resuming.

How do I check what ran?

Start with the run summary and output files. OncoTracer records the commands, tool versions, and completion status alongside the results. To show the installed OncoTracer version and source identity:

oncotracer provenance --json

For developers

Implementation details cover software packaging, cache verification, and installation safety. Release validation describes the automated comparisons. Neither page is needed to start an analysis.