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skills

skills is a skill for Claude Code, Codex from Babajan-B/BioQC-MCP. It costs 0 tokens per session (335 once invoked), scanned A, original, MIT.

A collection of reusable templates for checking the quality of FASTQ files, a common format for raw DNA sequencing data. The templates cover complete checks, batch analysis, and quick overviews.

In plain words
What is it for?
Use it to adapt a full quality check, process multiple samples, or get a fast sanity check of FASTQ files with the run_qc_pipeline tool.
Why use it?
It avoids having to design a quality-control workflow from scratch for every sequencing project.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 1repo 11mo ago A scan 0 tokens original MIT

Good fit Use it to adapt a full quality check, process multiple samples, or get a fast sanity check of FASTQ files with the run_qc_pipeline tool.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/babajan-b/bioqc-mcp/skills
View source ↗ Babajan-B/BioQC-MCP
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 Babajan-B/BioQC-MCP --skill skills
Clone the repo
git clone --depth 1 https://github.com/Babajan-B/BioQC-MCP

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 skills

README.md
[![agentmods](https://agentmods.dev/badge/skills/babajan-b/bioqc-mcp/skills/github.svg)](https://agentmods.dev/skills/babajan-b/bioqc-mcp/skills)
Your own site
<a href="https://agentmods.dev/skills/babajan-b/bioqc-mcp/skills"><img src="https://agentmods.dev/badge/skills/babajan-b/bioqc-mcp/skills/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.

agentmods 80×15 button for skills

Your own site · 80×15
<a href="https://agentmods.dev/skills/babajan-b/bioqc-mcp/skills"><img src="https://agentmods.dev/badge/skills/babajan-b/bioqc-mcp/skills.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 335 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 original 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 $0.00000 $0.00335
Opus 5.5 $0.00000 $0.00134
Sonnet 5.5 $0.00000 $0.00067
Haiku 4.5 $0.00000 $0.00034

Measured 2mo ago against content hash 924885385d35, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

skills 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.

The scan reads SKILL.md. This mod also ships 3 executable files (batch_analysis.py, full_qc_pipeline.py, quick_check.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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/SKILL.md · 41 lines

What it actually says

BioQC-MCP Skills

This directory contains reusable pipeline templates for the run_qc_pipeline tool.

Available Skills

Skill Description Use Case
full_qc_pipeline.py Complete QC workflow Analyze all FASTQ files in a directory
batch_analysis.py Multi-sample batch processing Process many samples with summary stats
quick_check.py Fast quality overview Quick sanity check on samples

Usage

AI agents can read these skill files and adapt them for user requests:

# Example: User asks "Run QC on my samples"
# AI reads skills/full_qc_pipeline.py and adapts it:

files = list_fastq_files('/path/to/samples')
print(f"Found {len(files)} FASTQ files")

for f in files:
    result = run_fastqc([f['path']], output_dir='./qc_results')
    print(f"Analyzed: {f['name']}")

multiqc = run_multiqc('./qc_results', output_dir='./multiqc_report')
print(f"Report: {multiqc['report']}")

Token Savings

Using skills with run_qc_pipeline reduces token usage by 75-98%:

Workflow Without Skills With Skills Savings
Single file QC 2,000 tokens 500 tokens 75%
Multi-sample 8,000 tokens 600 tokens 92%
Full pipeline 15,000 tokens 300 tokens 98%
Files

What ships with it

3 files 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. 2mo ago First seen · 41 lines · 0 tokens per session scan A 924885385d35

Subscribe to this mod's changes

skills is a skill published in the GitHub repository Babajan-B/BioQC-MCP (1 stars, last pushed 11mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 335 tokens. 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.

Scientificexome-analysisexome-sequencingfastqcmcp-servermultiqcngs
Related

skills compared with skills from other repositories

skills next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
skillsBabajan-B/BioQC-MCPSkill111mo agoMITA0Claude Code, Codex
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paper-searchopenags/paper-search-mcpSkill3.0k1mo agoMITA78Claude Code, Codex
mitiq-error-mitigationxi-zhao/OpenQuantumSkill71yesterdayMITA48Claude Code, Codex
quantum-ground-statexi-zhao/OpenQuantumSkill71yesterdayMITA103Codex
qmclaw-workbenchxi-zhao/OpenQuantumSkill71yesterdayMITA124Codex