Borrowing it
Nothing to install: this file belongs to broadinstitute/viral-ngs. 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/broadinstitute/viral-ngs/main/CLAUDE.mdgit clone --depth 1 https://github.com/broadinstitute/viral-ngsWrote 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/broadinstitute/viral-ngs/claude-md)<a href="https://agentmods.dev/instructions/broadinstitute/viral-ngs/claude-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/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/broadinstitute/viral-ngs/claude-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/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 | $0.00323 | $0.00323 |
| Opus 5 | $0.00161 | $0.00161 |
| Sonnet 5 | $0.00065 | $0.00065 |
| Haiku 4.5 | $0.00032 | $0.00032 |
Grade A, and why
viral-ngs 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 10d 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
92% identical to viral-ngs copilot-instructions.md — 18 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.
What it actually says
CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
IMPORTANT: Always read AGENTS.md at the start of every session before doing any work. It contains comprehensive project context and development guidelines that are essential for working in this codebase.
Quick Reference
- Docker-centric development: Run tests inside containers, not on host
- Import pattern:
from viral_ngs import corethencore.samtools.SamtoolsTool() - Test location:
tests/unit/<module>/ - Dependencies: ALL via conda, not pip (see
docker/requirements/*.txt)
Running Tests
docker run --rm \
-v $(pwd):/opt/viral-ngs/source \
quay.io/broadinstitute/viral-ngs:main-core \
pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit
Key Files
| File | Purpose |
|---|---|
| AGENTS.md | Full AI assistant guidance |
| pyproject.toml | Package configuration |
| docker/ | Dockerfiles and requirements |
| src/viral_ngs/ | Source code |
| tests/ | Test files |
| .agents/skills/ | Reusable agent playbooks and scripts |
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.
- 10d ago First seen · 33 lines · 323 tokens per session scan A b22853cf7ba7
viral-ngs CLAUDE.md is an instructions file published in the GitHub repository broadinstitute/viral-ngs (197 stars, last pushed 7d ago), licensed MIT. It adds 323 tokens to every session, about $0.0016 per session on Opus 5. A static security scan graded it A with 0 findings. It is 92% identical to viral-ngs copilot-instructions.md, differing in 18 lines, and is treated as a copy.
Other instructions, from other repositories
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.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
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).
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
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.