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bio-metagenomics-strain-tracking

80 / 100 · Low risk

Fine to try.

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

Resolves and compares bacterial strains below the species level from shotgun metagenomes with inStrain (popANI/conANI microdiversity), StrainPhlAn (marker-SNV consensus phylogeny and nGD), MIDAS2, metaSNV, and StrainGE, plus genome-vs-genome ANI (skani/fastANI/MASH) for isolate/MAG comparison. Covers why a strain is a threshold not a thing, why ANI answers same-genome while popANI/nGD answer same-population-in-situ, the 99.999% popANI and per-species nGD definitions, the coverage detection limi…

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