AR
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Data & Repro
BI
bio-epidemiological-genomics-amr-surveillance
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epidemiological-genomics-amr-surveillance
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: amrfinder -n assembly.fasta --plus --organism Klebsiella.
- 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.
- conda install -c bioconda ncbi-amrfinderplus.
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- metagenomics/amr-detection - AMR from metagenomic samples
- epidemiological-genomics/pathogen-typing - Strain context for AMR
- variant-calling/variant-annotation - Point mutation resistance
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