Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/45ck/open-genome-agent/agents-mdgit clone --depth 1 https://github.com/45ck/open-genome-agentWhat 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 | $0.00712 | $0.00712 |
| Opus 5 | $0.00356 | $0.00356 |
| Sonnet 5 | $0.00142 | $0.00142 |
| Haiku 4.5 | $0.00071 | $0.00071 |
Grade A, and why
open-genome-agent AGENTS.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 yesterday.
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.
Copies of this mod
1 near-identical copy found in the catalogue:
- open-genome-agent CLAUDE.md — 95% identical, 10 lines differ
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.
AGENTS.md
Project guidance for Codex.
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.
- yesterday First seen · 142 lines · 712 tokens per session scan A 40049b7ea1e0
open-genome-agent AGENTS.md is an instructions file published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 2mo ago), licensed MIT. It adds 712 tokens to every session, about $0.0036 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
ClawBio AGENTS.md
AGENTS.md instructions for ClawBio/ClawBio, covering agents.md — clawbio guide for ai coding agents, project overview, setup, clone and install dependencies.
SciAgent-Skills AGENTS.md
AGENTS.md instructions for jaechang-hits/SciAgent-Skills, covering skills — workflow guide, directory layout, workflow: topic → entry (5 steps), step 2. choose category and step 3. gather reference material.
SciAgent-Skills CLAUDE.md
Claude Code instructions for jaechang-hits/SciAgent-Skills, a project described as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.
ClawBio CLAUDE.md
Claude Code instructions for ClawBio/ClawBio, covering claude.md — clawbio agent instructions, homepage (index.html) — strict, key files, slash commands and skill routing table.
mygene-mcp AGENTS.md
AGENTS.md instructions for nickzren/mygene-mcp, covering agent guide — mygene-mcp, what this server is, run locally (stdio), use this server for and triage hints.
mgi-link CLAUDE.md
Claude Code instructions for berntpopp/mgi-link, covering claude.md, tl;dr, common commands and layout.