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bio-metagenomics-metaphlan

95 / 100 · Low risk

Fine to try.

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

Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads). Covers why a MetaPhlAn percentage is a cell fraction (genome-size-normalized taxonomic abundance) and must never be merged with Kraken/Bracken read fractions, kSGB vs uSGB units for quantifying database-absent taxa, the unknown-fraction rescaling and its version-default flip, --index pinning as a batch variable, and when mOTUs3 or sourmash gat…

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-metaphlan' ] || [ -L ~/.agents/skills/'bio-metagenomics-metaphlan' ]; then echo 'A skill folder named bio-metagenomics-metaphlan 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-metagenomics-metaphlan' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-metagenomics-metaphlan' ~/.agents/skills/'bio-metagenomics-metaphlan' && 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-metaphlan' ~/.claude/skills/'bio-metagenomics-metaphlan' (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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