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bio-metagenomics-amr-detection

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-metagenomics-amr-detection🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomedetect

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-amr-detection

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: amrfinder -n assembly.fasta --organism Escherichia (AMRFinderPlus).
CLI: ResFinder, CARD/RGI for alternative database searches.
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.
amrfinder -n contigs.fasta -o amr_results.tsv --threads 8.

Source Doc

Excerpt From SKILL.md

Tool Comparison

Tool	Database	Best For
AMRFinderPlus	NCBI	Comprehensive, curated
ResFinder	CGE	Clinical isolates
CARD/RGI	CARD	Detailed resistance mechanisms
ABRicate	Multiple	Quick screening

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

Use cases

Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

metagenomics/kraken-classification - Taxonomic context
metagenomics/functional-profiling - Functional pathways
genome-assembly/contamination-detection - Sample QC
workflows/metagenomics-pipeline - Full metagenomics workflow

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