pathogen-variant-surveillance

92 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

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

Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target st…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this. Expected for a coding skill.

Found in 6 places.

skills/pathogen-variant-surveillance/SKILL.md, line 64cd skills/pathogen-variant-surveillance/scripts
skills/pathogen-variant-surveillance/SKILL.md, line 81python3 lineage_prevalence.py --top 5 --where country=USA --weeks 12
skills/pathogen-variant-surveillance/SKILL.md, line 93python3 resolve_lineage.py XFG.23.1.3 PQ.17 PC.2 NOTALINEAGE

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skills/pathogen-variant-surveillance/SKILL.md, line 113python3 lineage_prevalence.py "XFG.1.1*" "XFJ*" --where country=USA --weeks 16 --growth
skills/pathogen-variant-surveillance/SKILL.md, line 140python3 mutation_profile.py "XFJ*" --versus "XFG*" --gene S --since 2026-01-01
skills/pathogen-variant-surveillance/SKILL.md, line 157python3 reporting_lag.py --where country=USA

Connects to the internet

This is disclosed by the author in the skill's SKILL.md or README.

Found in 5 places.

skills/pathogen-variant-surveillance/scripts/lapis_client.py, line 45import urllib.request
skills/pathogen-variant-surveillance/scripts/lapis_client.py, line 167req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
skills/pathogen-variant-surveillance/scripts/lapis_client.py, line 172with urllib.request.urlopen(req, timeout=TIMEOUT) as response:

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skills/pathogen-variant-surveillance/scripts/lapis_client.py, line 290req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
skills/pathogen-variant-surveillance/scripts/lapis_client.py, line 292with urllib.request.urlopen(req, timeout=TIMEOUT) as response:

Install

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

if [ -e ~/.agents/skills/'pathogen-variant-surveillance' ] || [ -L ~/.agents/skills/'pathogen-variant-surveillance' ]; then echo 'A skill folder named pathogen-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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/pathogen-variant-surveillance' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/pathogen-variant-surveillance' ~/.agents/skills/'pathogen-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/'pathogen-variant-surveillance' ~/.claude/skills/'pathogen-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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Score history

Date	Version	Score
2026-11-11	`908229c`	92