bio-epidemiological-genomics-variant-surveillance
Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-variant-surveillance --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Nextclade 3.3+, ggplot2 3.5+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Variant Surveillance **"Classify my viral sequences into lineages"** → Assign pathogen lineages and track variants of concern using Nextclade or pangolin for real-time genomic surveillance. - CLI: `nextclade run -d sars-cov-2 -i sequences.fasta` - CLI: `pangolin sequences.fasta` for SARS-CoV-2 Pango lineage assignment ## Nextclade CLI ```bash # Install Nextclade npm install -g @nextstrain/nextclade # Or download binary curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o nextclade chmod +x nextclade # List available datasets nextclade dataset list # Download dataset (e.g., SARS-CoV-2) nextclade dataset get --name sars-cov-2 --output-dir data/sa
- Version Compatibility
- Nextclade CLI
- Pangolin for SARS-CoV-2
- Parse Nextclade Results
- Track Variants of Concern
- Mutation Analysis
- Surveillance Report
- Related Skills
Install Nextclade npm install -g @nextstrain/nextclade Or download binary curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o nextclade chmod +x nextclade List available datasets nextclade dataset list Download dataset (e.g., SARS-CoV-2) nextclade dataset get --name sars-cov-2 --output-dir data/sars-cov-2 Run analysis
What does the bio-epidemiological-genomics-variant-surveillance skill do?
Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-variant-surveillance --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.