---
name: borzoi
description: Use Borzoi-style regulatory genomics models for sequence-to-expression or variant-effect analysis. Use when the task asks for noncoding variant impact, regulatory sequence design, or expression prediction.
---

# Borzoi

Use this skill for regulatory genomics modeling around sequence, variant, and expression effects.

Workflow:

1. Pin genome build, interval coordinates, reference/alternate alleles, cell type or tissue, strand, and window size.
2. Confirm the model route: local checkpoint, managed endpoint, notebook package, or external documented service. Record missing checkpoints as setup work, not as a completed model run.
3. Build input FASTA/variant manifests with source URLs or accession IDs.
4. Save prediction arrays, summary tables, plots, model version, and runtime metadata as artifacts in the run output folder (`outputs/`).
5. Compare predicted effects against GTEx, ENCODE, literature, or other source-backed evidence when available.

Keep source-owned genomic coordinates separate from model-owned effect predictions in every output.