bio-metagenomics-amr-detection
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-amr-detection --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 Detection **"Screen my isolates for antibiotic resistance genes"** → Identify antimicrobial resistance determinants in bacterial genomes or metagenomes by searching against curated resistance gene databases. - CLI: `amrfinder -n assembly.fasta --organism Escherichia` (AMRFinderPlus) - CLI: ResFinder, CARD/RGI for alternative database searches Identify antimicrobial resistance (AMR) genes in bacterial genomes and metagenomes. ## Tool Comparison | Tool | Database | Best For | |------|----------|----------| | AMRFinderPlus | NCBI | Comprehensive, curated | | ResFinder | CGE | Clinical isolates | | CARD/RGI | CARD | Detailed resistance mechanisms | | ABRicate | Multiple | Quick screening | ## AMRFinderPlus (NCBI) #
- Version Compatibility
- Tool Comparison
- AMRFinderPlus (NCBI)
- Installation
- From Nucleotide Sequences
- From Protein Sequences
- Output Fields
- Batch Processing
- ResFinder
- Run ResFinder
- From Raw Reads (KMA)
- CARD/RGI
- Run RGI
- RGI Output
conda install -c bioconda ncbi-amrfinderplus amrfinder -u # Update database Assembled contigs amrfinder -n contigs.fasta -o amr_results.tsv --threads 8 With organism for point mutations amrfinder -n contigs.fasta -O Escherichia -o amr_results.tsv Include stress/virulence genes amrfinder -n contigs.fasta -O Salmonella --plus -o amr_results.tsv If you have predicted proteins amrfinder -p proteins.faa -o amr_results.tsv
What does the bio-metagenomics-amr-detection skill do?
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-amr-detection --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.