Borzoi
Predict gene expression and regulatory activity tracks from DNA sequences.
Installation
- Make sure Claude is on your device and in your terminal.
Skills load from
~/.claude/skills/when Claude Code starts up β so you need it on your machine first. If you don't have it yet, install it once with the command below, then runclaudein any terminal to verify.One-time setupnpm i -g @anthropic-ai/claude-codeAlready have it? Skip ahead.
- Paste into Claude Code or into your terminal.
This copies the whole skill folder into
~/.claude/skills/borzoi-aipoch/β the SKILL.md plus any scripts, reference docs, or templates the skill ships with. Safe default: works for every skill.Faster alternative (instruction-only skills)
Skips the clone and grabs only the SKILL.md file. Don't use this if the skill ships Python scripts, reference markdowns, or asset templates β they won't be downloaded and the skill will fail when it tries to load them.
Quick install (SKILL.md only)Sign up to copy - Restart Claude Code.
Quit and reopen Claude Code (or any other agent that loads from
~/.claude/skills/). New skills are picked up on startup. - Just ask Claude.
Skills auto-activate when your request matches the skill's description β no slash command needed. Trigger phrases live in the skill's own frontmatter; you can read them in the βWhat this skill doesβ section above.
Prefer to read the source first? Open on GitHub.
When Claude uses it
Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.
What this skill does
Borzoi β DNA β Functional Track Prediction
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.10+ | 3.11 |
| CUDA | 12.1+ | 12.4+ |
| GPU VRAM | 16 GB | 24 GB+ |
How to run
from borzoi_pytorch import Borzoi
model = Borzoi.from_pretrained("johahi/borzoi-replicate-0").cuda().eval()
# input: (batch, 4, 524288) one-hot DNA β output: (batch, tracks, 6144) bins
Borzoi consumes ~524 kb one-hot windows and emits binned predictions across
7,611 human tracks (the separate 2,608-track mouse head is off by default;
enable via enable_mouse_head=True and select with
forward(..., is_human=False)). For variant scoring, run ref/alt windows
centred on the variant and compare per-track output.
Output format
(B, T, L) tensor β T tracks Γ L 32-bp bins. Track metadata (assay,
biosample) is in borzoi_pytorch.pytorch_borzoi_model.TRACKS_DF (or model.tracks_df when using the AnnotatedBorzoi subclass) β the base Borzoi model has no targets attribute.
Remote compute
Needs β₯24 GB VRAM and either pre-cached HF weights or egress to
huggingface.co. Read compute_details({provider, mode:'read'}) for an
environment with borzoi-pytorch, then:
c = host.compute.create(provider)
job = c.submitJob(
intent="Borzoi track prediction for 1 locus β 1ΓGPU, ~2 min",
inputs=[{"src": "borzoi_run.py", "dstFilename": "borzoi_run.py"}],
command="python3 borzoi_run.py", # env selection is host-specific β see compute_details for your provider
outputs=["tracks.npz"],
timeoutSeconds=1800,
)
print(job.job_id) # cell ends here β kernel never blocks on compute
Retain the exact returned job_id. Query that saved ID with the non-blocking
c.attachJob(job_id).status() or .result() when its state or result is relevant; do not scan Job
history. A final .result() read reports whether its follow-up was suppressed or had already been
committed; otherwise the app starts the later analysis turn for an unread final result. See the
remote-compute-ssh skill for details.
If the provider exposes a weight-cache mount, point HF_HOME at it inside
borzoi_run.py (path is in compute_details).
Troubleshooting
| Symptom | Cause | Fix |
|---|---|---|
module has no __version__ | Package exposes no attr | Use importlib.metadata.version("borzoi-pytorch") |
| Shape mismatch on input | Wrong window length | Pad/crop to 524288 bp (fixed; not exposed as a model attribute) |
Next: combine track deltas with evo2 likelihood deltas for a
two-axis variant prioritisation.
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