AMR / Resistome Detection (bioSkills)

A Claude Code skill for detecting and quantifying antimicrobial-resistance genes in microbial communities from shotgun metagenomic reads, contigs, or MAGs.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT)
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash), not as an MCP tool
Verified	works · 2026-07-29
Security	cleared · 2026-07-29 — GPTomics/bioSkills MIT, amr-detection SKILL.md confirmed, provenance matches, read-only local workflow

How to install

bioSkills is not an npm package — clone the repo, then either run the installer for the whole category or copy the single skill directory.

Claude Code — clone and install via the bundled script:
```
git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "metagenomics"
```
The installer copies matching skills into ~/.claude/skills/ (default target). Use --list to preview and --dry-run to see what would be copied.
Claude Code / other agents — copy just this one skill:
```
cp -r bioSkills/metagenomics/amr-detection ~/.claude/skills/
```
(run from inside your clone; otherwise replace bioSkills/ with the absolute path of your clone). Install the resistome tools referenced by the skill (RGI, AMRFinderPlus, ABRicate, etc., via bioconda) and their databases (CARD, MEGARes, ResFinder) when prompted on first use.

What it does

Profiles the resistome — the antibiotic-resistance gene content of a community — via two complementary routes:

Read-based quantification — RGI bwt (CARD homolog mapping), AMR++/MEGARes (gene-fraction-filtered profiling), ARGs-OAP/SARG (normalized to copies per 16S / per cell), deepARG (deep-learning detection of divergent ARGs), GROOT (variation-graph typing of SNP-bearing alleles).
Presence calling on assemblies — AMRFinderPlus (curated per-gene thresholds) and ABRicate (rapid 80/80 contig screening) on contigs or MAGs.

The skill stresses a key caveat: an ARG hit is a sequence match, not a phenotype, and a metagenomic ARG has no host or genomic context until assembly — so breadth-of-coverage filtering is used to reject partial-domain false positives.

Primary use cases: community resistome quantification, ARG presence calling on contigs/MAGs, cross-sample ARG normalization, false-positive control.

Notes

Distributed as a SKILL.md in the bioSkills collection — Claude executes the workflow locally via Bash rather than as an MCP server. Upstream front-matter name: bio-metagenomics-amr-detection. Reference databases (CARD, MEGARes, ResFinder) are separate downloads. This is the first Claude-installable AMR/resistome wrapper the catalog has surfaced (previously a tracked gap). Upstream directory: metagenomics/amr-detection.

Sources

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