vdjdb-extract

vdjdb-extract is a skill for Claude Code, Codex from antigenomics/vdjdb-db. It costs 56 tokens per session (3,599 once invoked), scanned A, original, AGPL-3.0.

A procedure for extracting T-cell receptor and immune-target relationships from source files such as research papers, spreadsheets, PDFs, 10x output, and AIRR files. It produces a VDJdb-formatted tab-separated data chunk.

In plain words
What is it for?
Use it to collect receptor-to-target data from publications, supplementary tables, XLS files, PDFs, 10x experiments, or AIRR-format files.
Why use it?
The needed records may be buried in documents or stored in incompatible formats. This turns those sources into a common structure for later formatting and review.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to collect receptor-to-target data from publications, supplementary tables, XLS files, PDFs, 10x experiments, or AIRR-format files.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/antigenomics/vdjdb-db/vdjdb-extract
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.

Any agent
npx skills add antigenomics/vdjdb-db --skill vdjdb-extract
Clone the repo
git clone --depth 1 https://github.com/antigenomics/vdjdb-db

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for vdjdb-extract

README.md
[![agentmods](https://agentmods.dev/badge/skills/antigenomics/vdjdb-db/vdjdb-extract.svg)](https://agentmods.dev/skills/antigenomics/vdjdb-db/vdjdb-extract)
Your own site
<a href="https://agentmods.dev/skills/antigenomics/vdjdb-db/vdjdb-extract"><img src="https://agentmods.dev/badge/skills/antigenomics/vdjdb-db/vdjdb-extract.svg" alt="Measured on agentmods" height="20"></a>
Per session 56 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,599 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
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 5.1 $0.00056 $0.03599
Opus 5 $0.00028 $0.01800
Sonnet 5 $0.00011 $0.00720
Haiku 4.5 $0.00006 $0.00360

Measured 8d ago against content hash 77a15ff38883, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

vdjdb-extract 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 8d 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.

skills/vdjdb-extract/SKILL.md · 231 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

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. 8d ago First seen · 231 lines · 56 tokens per session scan A 77a15ff38883

Subscribe to this mod's changes

vdjdb-extract is a skill published in the GitHub repository antigenomics/vdjdb-db (155 stars, last pushed 12d ago), licensed AGPL-3.0. It adds 56 tokens to every session and 3,599 once invoked, about $0.0003 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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