QuickStart 1: Illumina and ONT

Open this guide with playable videos

Analyze libraries for copy-number changes (CNA). Choose Illumina, ONT or both in separate projects. Reads total approximately 225 MB, plus tools, references and results. FASTQs alone cannot assess ONT methylation.

With the current GitHub source, select ONT/: each named folder is one intended library and supplies its sample name. This named layout is newer than PyPI 2.1.0.

ONT/
├── ONCO-001/
│   ├── fastq_pass/
│   ├── fastq_fail/
│   ├── pod5_pass/
│   ├── pod5_fail/
│   └── bam_pass/       # or modified_bam/
└── ONCO-002/
    ├── fastq_pass/
    ├── fastq_fail/
    ├── pod5_pass/
    ├── pod5_fail/
    └── bam_pass/       # or modified_bam/

Methylation automatically links each named library's pod5_pass. The browser lists its ONCO-style name; drag samples to MARLIN or Sturgeon using clinical records. Saved or explicitly selected modified-base BAMs remain valid alternatives.

CNA/variants use only fastq_pass. Other folders are optional; methylation needs matching MM/ML modified-base BAMs or POD5 plus compatible Dorado models. FASTQs contain no methylation marks. The downloads/videos below use the supported legacy fastq_pass/barcode01 layout; single MinKNOW runs and ligation libraries also remain supported. ONT layout and settings.

Installation · Terminal commands.

1. Interactive launch

Choose CPU/RAM budgets and concurrent sample counts before saving. Multiple samples and continuation.

Download and verify the reads before choosing inputs. Open setup:

oncotracer --interactive --backend conda

Or use Nextflow from the source checkout:

nextflow run main.nf --interactive --backend conda

Use the full path to main.nf from another directory. For Docker, use --backend docker. Choose 1. New analysis for setup, or 2. Continue an existing analysis for saved work (video). Run analysis starts the work. These videos use synthetic inventories and checks.

Illumina

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ONT

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Example data: download and verify

Replace /path/to/my/analyses_dir/ with your writable analysis directory in every block. $PWD means that directory's absolute path.

cd /path/to/my/analyses_dir/
mkdir -p oncotracer-quickstart1/input/illumina \
  oncotracer-quickstart1/input/fastq_pass/barcode01

curl --fail --location --continue-at - \
  --output oncotracer-quickstart1/input/illumina/ERR12341627_1.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/027/ERR12341627/ERR12341627_1.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart1/input/illumina/ERR12341627_2.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/027/ERR12341627/ERR12341627_2.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart1/input/fastq_pass/barcode01/DRR165691_1.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR165/DRR165691/DRR165691_1.fastq.gz

md5sum -c <<'MD5'
4c96d551152694b3893ea98b7781a3ae  oncotracer-quickstart1/input/illumina/ERR12341627_1.fastq.gz
1b20d9eb98f755244f6383ea1354bd40  oncotracer-quickstart1/input/illumina/ERR12341627_2.fastq.gz
55a3984cb0334aa4cb0a38255cb71c06  oncotracer-quickstart1/input/fastq_pass/barcode01/DRR165691_1.fastq.gz
MD5

Require three checksum OK lines. Repeat interrupted curl commands to resume. The ONT folder is barcode01.

2. Terminal questions for headless servers

Over SSH, choose one setup route per project. These videos use synthetic FASTQs without running analysis; use the verified public downloads above.

Illumina

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ONT

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Answer the questions

These commands supply the project, platform and input folder; the wizard asks for the remaining settings. Press Enter to accept a displayed default.

Illumina

cd /path/to/my/analyses_dir/
oncotracer setup --terminal --backend conda \
  --project "$PWD/oncotracer-quickstart1/illumina" \
  --mode illumina --input-folder "$PWD/oncotracer-quickstart1/input/illumina"

ONT

cd /path/to/my/analyses_dir/
oncotracer setup --terminal --backend conda \
  --project "$PWD/oncotracer-quickstart1/ont" \
  --mode ont --input-folder "$PWD/oncotracer-quickstart1/input/fastq_pass"

For an installed Docker backend, use --backend docker. Select all, assign cancer, and choose cna:

Project	Sample name	CNA settings
Illumina	Keep ERR12341627	QDNAseq; answer 100 kb
ONT	Rename barcode01 to DRR165691	Choose ichorcna; fixed 500 kb

All FASTQ batches inside barcode01 form one sample. Set a CPU budget, for example 4, and answer no to interpretation reports and small variants. CNA-only terminal setup does not ask Fresh/FFPE; preservation is asked when enabling variants.

For hg38 reference, choose download, or reuse and give a prepared reference folder. With download selected, the first analysis downloads about 8.0 GiB for Illumina or 9.7 GiB for ONT; setup does not download indexes. See genome indexes.

At Final action, enter save. Review the checked configuration and sample names. When ready, launch the printed oncotracer run command in your terminal.

3. Read the results

When finished, click Open results in the browser or open results/index.html. Files are under oncotracer-quickstart1/illumina/results/ or oncotracer-quickstart1/ont/results/:

File	Purpose
index.html	Results dashboard
06_workflow_summary/workflow_summary.txt	Completion status
06_workflow_summary/final_report.html	Combined findings
03_cna_codification/cna_events.tsv	Copy-number changes
04_cna_custom_plots/cna_per_sample_pages.pdf	Sample plots
.oncotracer-native/trace.tsv	Recorded commands

Stop or resume

For a terminal run, press Ctrl+C; use tmux to keep a remote run alive after disconnecting. For a browser run, use Stop analysis, wait for it to stop, and choose No in Delete incomplete run?. Closing its browser or setup terminal does not stop that analysis.

Follow Run, stop and resume with the saved project path. Valid completed steps are reused. Concurrent runs need separate projects and a share of the server's CPU and memory.

Next: your own samples or QuickStart 2: HCC1143.

For automated setup and terminal execution, use the complete terminal commands.