CLI: PCR Amplicon DAGs

Helix now ships an in‑silico PCR workflow that produces the same provenance‑stamped DAG artifacts as the CRISPR and Prime editors. Each branch captures primer binding, per-cycle amplification, and optional error events so you can visualize how an amplicon population evolves over time.

This walkthrough uses the bundled plasmid FASTA plus the sample configs in examples/pcr_*.json. Everything stays simulation-only—no wet-lab instructions or thermocycler recipes are provided.

Primer + PCR configs

File	Purpose
`examples/pcr_primers.json`	Defines a primer pair (`forward`/`reverse`) with optional metadata and mismatch tolerances.
`examples/pcr_config.json`	Captures high-level parameters such as cycle count, per-cycle efficiency, error rate, and amplicon length bounds.

Primer schema (excerpt):

{
  "name": "demo_pcr",
  "forward": {
    "name": "demo_forward",
    "sequence": "ATGCGTACGTTG",
    "max_mismatches": 0
  },
  "reverse": {
    "name": "demo_reverse",
    "sequence": "CGGTCAACGTAC",
    "max_mismatches": 0
  },
  "metadata": {
    "use_case": "demo"
  }
}

PCR configuration schema (excerpt):

{
  "cycles": 6,
  "per_cycle_efficiency": 0.85,
  "error_rate": 0.0005,
  "min_amplicon_length": 80,
  "max_amplicon_length": 500,
  "max_amplicons": 32
}

Generate an amplicon DAG

python -m helix.cli pcr dag \
  --genome src/helix/datasets/dna/plasmid_demo.fna \
  --primer-config examples/pcr_primers.json \
  --pcr-config examples/pcr_config.json \
  --out pcr_amplicon_dag.json

The output is a standard Helix DAG artifact (helix.pcr.amplicon_dag.v1). Nodes store fully materialized genome views, stages (root, binding, cycled, error, …), log probabilities, and primer metadata. The artifact feeds directly into:

python -m helix.cli edit-dag viz --input pcr_amplicon_dag.json --out pcr_dag.png
python -m helix.cli edit-dag animate --input pcr_amplicon_dag.json --out pcr_dag.gif --fps 6

Playground link

Want to inspect the DAG interactively? The playground accepts any hosted JSON via the ?json= parameter. The docs site publishes the demo artifact generated above, so you can open:

https://omniscoder.github.io/Helix/playground/?json=assets/viz/pcr_amplicon_dag.json

Inside the playground you can:

Drag to pan/zoom, toggle layouts, or filter by probability/time-step.
Click nodes to see stage metadata plus root→node sequence diffs.
Export a PNG snapshot or copy the shareable link with the ?json= payload.

You can also drag-drop your own helix.pcr.amplicon_dag.v1 file right into the browser.

Chaining PCR after CRISPR/Prime

Because all edit engines emit compatible DAG artifacts, you can combine workflows end-to-end:

Use helix crispr dag or helix prime dag to model genome edits.
Feed the edited genome (or specific branches) into the PCR simulator.
Visualize everything via helix edit-dag viz/animate or the playground for side-by-side comparisons.

Pair this with helix workflows to automate CRISPR → PCR → visualization pipelines in a single YAML config.