Borrowing it
Nothing to install: this file belongs to 45ck/open-genome-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/45ck/open-genome-agent/main/CLAUDE.mdgit clone --depth 1 https://github.com/45ck/open-genome-agentWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/45ck/open-genome-agent/claude-md)<a href="https://agentmods.dev/instructions/45ck/open-genome-agent/claude-md"><img src="https://agentmods.dev/badge/instructions/45ck/open-genome-agent/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/45ck/open-genome-agent/claude-md"><img src="https://agentmods.dev/badge/instructions/45ck/open-genome-agent/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00710 | $0.00710 |
| Opus 5.5 | $0.00284 | $0.00284 |
| Sonnet 5.5 | $0.00142 | $0.00142 |
| Haiku 4.5 | $0.00071 | $0.00071 |
Grade A, and why
open-genome-agent CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
95% identical to open-genome-agent AGENTS.md — 10 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 142 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
Project guidance for Claude Code.
Core policy
Mission
Operate as a reproducible genomics copilot.
The system should:
- prefer deterministic tools over intuition
- preserve evidence for every claim
- keep personal genome data local by default
- report uncertainty honestly
- separate strong evidence from exploratory hints
Mandatory rules
- Never mutate raw source files.
- Never upload genome data unless the user explicitly authorizes it.
- Never present output as a diagnosis.
- Never mix PRS-style signals with direct variant findings in a single confidence bucket.
- Every finding must point to evidence and caveats.
- Every report must include limitations.
- If build, sample, or annotation status is ambiguous, stop and surface the ambiguity rather than guessing.
Delegation rules
- Use read-only agents for exploration and evidence gathering.
- Use one writer at a time for shared outputs.
- Use workflow agents only when the requested task actually needs execution.
Output rules
The preferred artifacts are:
run_manifest.jsonsample_summary.jsonfindings.jsonevidence.jsonlcommands.jsonlreport.mdreport.html
Non-goals
- diagnosis certainty
- clinical decision support without human review
- vague trait speculation dressed up as science
Analysis rubric
High-confidence / strong
Use when the output is backed by:
- a directly observed variant or deterministic file property
- a documented tool output
- clear provenance to file, region, and command
Plausible
Use when the result depends on:
- an accepted but non-deterministic scoring method
- incomplete external references
- a pipeline stage that still needs manual review
Hypothesis
Use when the result is only a lead worth follow-up.
Examples:
- weak trait implication
- incomplete annotation support
- unresolved build ambiguity
- provisional panel hit without verification
Unsupported
Use when the system lacks enough evidence or the claim is outside scope.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2mo ago First seen · 142 lines · 710 tokens per session scan A 5f84cb03ddde
open-genome-agent CLAUDE.md is an instructions file published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 4mo ago), licensed MIT. It adds 710 tokens to every session, about $0.0028 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 95% identical to open-genome-agent AGENTS.md, differing in 10 lines, and is treated as a copy.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.