bio-epidemiological-genomics-amr-surveillance
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-amr-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: AMRFinderPlus 3.12+, 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. # AMR Surveillance **"Screen my isolates for resistance genes and track AMR trends"** → Detect antimicrobial resistance determinants in bacterial genomes and monitor resistance patterns over time for surveillance programs. - CLI: `amrfinder -n assembly.fasta --plus --organism Klebsiella` ## AMRFinderPlus ```bash # Install AMRFinderPlus conda install -c bioconda ncbi-amrfinderplus # Update database amrfinder -u # Basic AMR detection from genome amrfinder -n genome.fasta -o results.tsv # With protein input (faster, more sensitive) amrfinder -p proteins.faa -o results.tsv # Specify organism for point mutations amrfinder -n genome.fasta --organism Salmonella -o results.tsv # Available organisms: Acinetobacter_baumannii,
- Version Compatibility
- AMRFinderPlus
- Parse AMRFinder Results
- ResFinder Alternative
- Track Resistance Trends
- Clinical Interpretation
- Surveillance Report
- Related Skills
Install AMRFinderPlus conda install -c bioconda ncbi-amrfinderplus Update database amrfinder -u Basic AMR detection from genome amrfinder -n genome.fasta -o results.tsv With protein input (faster, more sensitive) amrfinder -p proteins.faa -o results.tsv Specify organism for point mutations amrfinder -n genome.fasta --organism Salmonella -o results.tsv
What does the bio-epidemiological-genomics-amr-surveillance skill do?
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-amr-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.