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bio-metagenomics-contamination-controls

95 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

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-c…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-metagenomics-contamination-controls' ] || [ -L ~/.agents/skills/'bio-metagenomics-contamination-controls' ]; then echo 'A skill folder named bio-metagenomics-contamination-controls already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-metagenomics-contamination-controls' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-metagenomics-contamination-controls' ~/.agents/skills/'bio-metagenomics-contamination-controls' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-metagenomics-contamination-controls' ~/.claude/skills/'bio-metagenomics-contamination-controls' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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