claw-metagenomics

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill claw-metagenomics --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Shotgun Metagenomics Profiler Comprehensive shotgun metagenomics analysis combining taxonomic classification, antimicrobial resistance gene detection, and functional pathway profiling from paired-end FASTQ files. ## What it does 1. Takes paired-end FASTQ files (R1, R2) or a single concatenated FASTQ as input 2. Runs **Kraken2** taxonomic classification against a standard database (e.g., Standard-8, PlusPF) 3. Refines abundances with **Bracken** at species level (read re-estimation) 4. Detects antimicrobial resistance genes with **RGI** against the **CARD** database 5. Classifies detected ARGs by **WHO critical priority pathogen** association 6. Optionally runs **HUMAnN3** for functional pathway profiling (MetaCyc + UniRef) 7. Generates three publication-quality figures: - **Figure 1**: Taxonomy bar chart — top 20 species by relative abundance - **Figure 2**: Resistome heatmap — ARG families by drug class with abundance - **Figure 3**: WHO-critical ARG summary — priority-tier breakdown of detected resistance genes 8. Produces a full reproducibility bundle (commands.sh, environment.yml, checksums.sha256) ## Why this exists If you ask a general AI to "analyse a metagenome," it will:

Full pipeline (taxonomy + resistome + functional)
python metagenomics_profiler.py \
Skip HUMAnN3 (faster — taxonomy + resistome only)
Single concatenated FASTQ
Specify Kraken2 database path
python metagenomics_profiler.py --demo --output demo_report