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bio-epidemiological-genomics-variant-surveillance

80 / 100 · Low risk

Fine to try.

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

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode …

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