Bio Metagenomics Contamination Controls
Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and decontam, mock-community validation, and depth-adequacy checks (Nonpareil). Covers why a metagenomic result is a position in a choice-chain rather than a direct observation, why extraction is the experiment, why a low-biomass community can be entirely kitome, why absence means not-detectable-by-this-chain, and why a confident classifier call can still be wrong when the reference is contaminated. Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
Security AStatic scan found no risk patternsHow grading works ›
What this skill does
Bio Metagenomics Contamination Controls is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-metagenomics-contamination-controls/ and loads when your prompt matches the skill's trigger.
When to invoke it: Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
Who uses this skill
The Bio Metagenomics Contamination Controls Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 161,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
How to install
Free
Manual install (2 steps)
mkdir -p ~/.claude/skills/bio-metagenomics-contamination-controls
curl -L https://claudskills.com/skills/bio-metagenomics-contamination-controls/SKILL.md \
-o ~/.claude/skills/bio-metagenomics-contamination-controls/SKILL.md
Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-metagenomics-contamination-controls/. Claude Code auto-discovers it on next session.
Skills live at ~/.claude/skills/bio-metagenomics-contamination-controls/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-metagenomics-contamination-controls\SKILL.md on Windows. See the full install guide for step-by-step instructions.
Telegram
📱 Install from your phone or desktop Telegram
Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →
Pro
One-click install via the desktop app
The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.
Pro
For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.
Frequently asked questions
How do I install the Bio Metagenomics Contamination Controls Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy
SKILL.md from the source repository to
~/.claude/skills/bio-metagenomics-contamination-controls/SKILL.md and restart Claude Code. Both flows are detailed at
claudskills.com/install/.
What does the Bio Metagenomics Contamination Controls skill do?
Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and decontam, mock-community validation, and depth-adequacy checks (Nonpareil). Covers why a metagenomic result is a position in a choice-chain rather than a direct observation, why extraction is the experiment, why a low-biomass community can be entirely kitome, why absence means not-detectable-by-this-chain, and why a confident classifier call can still be wrong when the reference is contaminated. Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the Bio Metagenomics Contamination Controls skill?
Use Bio Metagenomics Contamination Controls when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Bio Metagenomics Contamination Controls" or describe the task and let Claude pick). Browse related skills at
/category/science/.
What is a Claude Code skill and how does the Bio Metagenomics Contamination Controls skill fit in?
A Claude Code skill is a
SKILL.md file that lives under
~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Bio Metagenomics Contamination Controls is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at
/learn/what-is-a-claude-skill/.
Attribution & license
Cite this skill
If you reference this skill in a blog post, paper, or documentation, you can cite it as:
APA
bg-szy. (2026). Bio Metagenomics Contamination Controls [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-metagenomics-contamination-controls/
BibTeX
@misc{bio-metagenomics-contamination-controls-2026,
author = {bg-szy},
title = {Bio Metagenomics Contamination Controls [Claude Code skill]},
year = {2026},
publisher = {ClaudSkills},
url = {https://claudskills.com/skills/bio-metagenomics-contamination-controls/}
}Embed this skill
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Security scan
Grade A · scanned 2026-07-26 — free static scan against the OWASP Agentic Skills Top 10.
No risk patterns were found in any of the ten OWASP-aligned categories. How grading works ›
- ✓ Prompt injection
- ✓ Data exfiltration
- ✓ Supply chain
- ✓ Reverse shell
- ✓ Credentials
- ✓ Execution
- ✓ Filesystem
- ✓ Persistence
- ✓ Obfuscation
- ✓ Network
Show this grade on your repo (click to copy):
[](https://claudskills.com/skills/bio-metagenomics-contamination-controls/#security)
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