cite-encode

A guide for creating correct citations and acknowledgments for ENCODE data. ENCODE is a public project that provides genomic research data and has rules for how its data should be credited.

In plain words
What is it for?
Use it when writing a paper, grant, presentation, bibliography, or acknowledgment section that uses ENCODE data.
Why use it?
It helps avoid missing required credit or using inconsistent bibliography entries when sharing research based on ENCODE data.

Skill for Claude CodeCodex

Install

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.

agentmods
npx agentmods add skills/ammawla/encode-toolkit/cite-encode
Any agent
npx skills add ammawla/encode-toolkit --skill cite-encode
Clone the repo
git clone --depth 1 https://github.com/ammawla/encode-toolkit

Made for: Claude Code, Codex.

Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,130 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5 $0.00046 $0.08130
Opus 5 $0.00023 $0.04065
Sonnet 5 $0.00009 $0.01626
Haiku 4.5 $0.00005 $0.00813

Measured 2d ago against content hash 5749e2ca4d01, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

cite-encode 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 2d 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.

plugin/skills/cite-encode/SKILL.md · 644 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

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.

  1. 2d ago First seen · 644 lines · 46 tokens per session scan A 5749e2ca4d01

Subscribe to this mod's changes

cite-encode is a skill published in the GitHub repository ammawla/encode-toolkit (24 stars, last pushed 1mo ago), licensed AGPL-3.0. It adds 46 tokens to every session and 8,130 once invoked, about $0.0002 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 2026-08-30.

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