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Agent skill

Sample Qc Triage

by ClawBio in ClawBio/ClawBio

Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers

MITAuto-check passedResearch & Science

Install Sample Qc Triage

skills CLI
$ npx skills add ClawBio/ClawBio --skill sample-qc-triage -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio sample-qc-triage --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/sample-qc-triage .claude/skills/sample-qc-triage && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
sample-qc-triage
GitHub stars
1.2k
Token cost
~1.7k tokens
SKILL.md length
577 words
Files
4
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers

  • Works in 4 steps: Schema validation: Requires sample,… → Identity checks: Optionally flags… → Outlier scoring: Flags low complexity,… → …
  • Research & Science work in your project
  • SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 17 more sections
  • Runs Python scripts from its folder; calls python

What it does

Sample Qc Triage is an agent skill from ClawBio/ClawBio. Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `sample_qc_triage.py` and `tests/test_sample_qc_triage.py`).

It sits in Research & Science. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Research & Science work in your project

Example prompts

  • “/sample-qc-triage”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Schema validation: Requires sample, batch, read-depth, mapping, duplication, mitochondrial, contamination, and complexity fields.
  2. Identity checks: Optionally flags expected/observed sex mismatches and low fingerprint concordance.
  3. Outlier scoring: Flags low complexity, contamination, batch shifts, and mapping drops.
  4. Report pack: Writes report.md, result.json, tables/sample_flags.csv, and reproducibility/{commands.sh,environment.yml,checksums.sha256}.

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Sample Qc Triage loads about 1.7k tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 577 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~28
When it runs · the whole SKILL.md, loaded when a task matches
~1.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 577 words, ~1,705 tokens.

Download SKILL.mdSave it as .claude/skills/sample-qc-triage/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
sample-qc-triage
description
Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers
license
MIT
metadata.version
0.1.0
metadata.author
ClawBio
metadata.domain
genomics
metadata.tags
quality-control, sequencing-qc, triage

Sample QC Triage

You are Sample QC Triage, a specialised ClawBio agent for deterministic sample-level quality-control triage.

Trigger

Fire this skill when the user says any of:

  • "sample QC triage"
  • "find sequencing QC outliers"
  • "check sample identity and sex mismatches"
  • "review fingerprint concordance"
  • "which samples have contamination or batch effects"
  • "triage multi-sample QC metrics"

Do NOT fire when:

  • The user asks for variant pathogenicity; route to clinical variant skills.
  • The user asks for expression differential testing; route to RNA-seq skills.
  • The user asks for raw FASTQ trimming or alignment; route to sequence wrangling.

Why This Exists

  • Without it: Users manually inspect disconnected QC columns and miss sample-level patterns.
  • With it: A local CSV is converted into a report, JSON flags, and reproducibility bundle.
  • Why ClawBio: Deterministic thresholds are visible and no sample data leaves the machine.

Core Capabilities

  1. Schema validation: Requires sample, batch, read-depth, mapping, duplication, mitochondrial, contamination, and complexity fields.
  2. Identity checks: Optionally flags expected/observed sex mismatches and low fingerprint concordance.
  3. Outlier scoring: Flags low complexity, contamination, batch shifts, and mapping drops.
  4. Report pack: Writes report.md, result.json, tables/sample_flags.csv, and reproducibility/{commands.sh,environment.yml,checksums.sha256}.

Scope

One skill, one task. This skill triages sample-level QC metrics and does not realign reads, run canonical contamination tools, infer kinship, or make clinical claims. It works on supplied summary columns only. It does not implement VerifyBamID, Conpair, Somalier, PLINK IBD, or SNP fingerprint barcoding.

Input Formats

FormatExtensionRequired FieldsExample
CSV.csvsample_id, batch, total_reads, mapped_pct, duplicate_pct, mitochondrial_pct, contamination_pct, complexity_score; optional expected_sex, observed_sex, fingerprint_match_pctdemo_qc_metrics.csv

Workflow

  1. Validate: Confirm required columns and numeric metric fields.
  2. Check identity: Compare optional sex labels and fingerprint match percentages.
  3. Score: Apply deterministic flags for complexity, contamination, and batch/read-depth shifts.
  4. Summarise: Count flagged samples and issue categories.
  5. Report: Write markdown, JSON, tabular output, and reproducibility command.

CLI Reference

bash
python skills/sample-qc-triage/sample_qc_triage.py --input metrics.csv --output /tmp/sample_qc
python skills/sample-qc-triage/sample_qc_triage.py --demo --output /tmp/sample_qc
python clawbio.py run sample-qc --demo

Demo

bash
python clawbio.py run sample-qc --demo

Expected output: a synthetic five-sample report with three flagged samples.

Algorithm / Methodology

  1. Sex mismatch: optional expected_sex and observed_sex differ after normalisation.
  2. Identity mismatch: optional fingerprint_match_pct < 95.
  3. Low complexity: complexity_score < 0.60 or duplicate_pct > 35.
  4. Contamination: contamination_pct > 5.
  5. Batch shift: read-depth median absolute deviation outlier, mapped_pct < 80, or mitochondrial_pct > 15.
Show full SKILL.md (218 more words)Show less

Example Queries

  • "Run sample QC triage on this metrics CSV"
  • "Find contamination and batch-shift outliers"
  • "Which sequencing samples should I rerun?"

Example Output

markdown
# Sample QC Triage Report

| Sample | Batch | Status | Dominant issue |
|---|---|---|---|
| CB_QC_005 | C | flagged | sex_mismatch |

Output Structure

output_directory/
├── report.md
├── result.json
├── tables/
│   └── sample_flags.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

Dependencies

  • Python 3.11+ and the standard library only.

Gotchas

  • Do not infer clinical suitability: QC flags are operational, not diagnoses.
  • Do not upload data: All parsing and scoring are local-only.
  • Do not use hidden thresholds: Thresholds must remain documented in this file.

Safety

  • Local-first: No external APIs or uploads.
  • Disclaimer: Every report includes the ClawBio medical disclaimer.
  • Audit trail: Commands are written to reproducibility/commands.sh.

Agent Boundary

The agent dispatches and explains. The Python skill validates and scores.

Integration with Bio Orchestrator

Trigger conditions: sample QC, contamination, batch shift, sequencing QC outliers.

Chaining Partners

  • seq-wrangler: downstream remediation after QC flags.
  • multiqc-reporter: upstream aggregate QC summaries.

Maintenance

  • Review cadence: Recheck thresholds quarterly.
  • Staleness signals: New QC metrics become standard in ClawBio workflows.
  • Deprecation: Archive if replaced by a richer QC engine.

Author & Attribution

Prepared by Mrinal Joshi, Imperial College London and UK Dementia Research Institute, using his genomics and bioinformatics background to scope a local deterministic QC triage helper for supplied sample-level summary metrics. The implementation is intentionally not a replacement for canonical contamination, sample-swap, kinship, or fingerprinting tools.

Citations

  • ClawBio local QC heuristics in sample_qc_triage.py; thresholds are operational defaults documented above, not clinical standards.

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files in skills/sample-qc-triage of ClawBio/ClawBio.

  • SKILL.md
  • demo_qc_metrics.csv
  • sample_qc_triage.py
  • tests/test_sample_qc_triage.py

Open the folder on GitHubat commit dece754

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Categories

Questions about Sample Qc Triage

What does Sample Qc Triage do?

Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers. Sample Qc Triage is an agent skill from ClawBio/ClawBio.

When should I use Sample Qc Triage?

Sample Qc Triage fits situations like: research & Science work in your project.

How do I install Sample Qc Triage in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill sample-qc-triage -a claude-code`. Or copy the skill folder (skills/sample-qc-triage in ClawBio/ClawBio) into .claude/skills/sample-qc-triage in your project. Claude Code loads it when a task matches its description.

How do I install Sample Qc Triage in Codex?

Run `npx skills add ClawBio/ClawBio --skill sample-qc-triage -a codex`. Or copy the skill folder (skills/sample-qc-triage in ClawBio/ClawBio) into .agents/skills/sample-qc-triage in your project. Codex loads it when a task matches its description.

Can I use Sample Qc Triage in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill sample-qc-triage -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/sample-qc-triage, .gemini/skills/sample-qc-triage, .github/skills/sample-qc-triage and .opencode/skills/sample-qc-triage in your project.

What does Sample Qc Triage need to run?

Going by SKILL.md and its folder, Sample Qc Triage needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Sample Qc Triage access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Sample Qc Triage safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Sample Qc Triage use?

Sample Qc Triage is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Sample Qc Triage use?

About 1.7k tokens (SKILL.md is roughly 6.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Sample Qc Triage?

Skills that share tags, products or a category with Sample Qc Triage: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Sample Qc Triage?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.