claw-metagenomics
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
npx skills add BioTender-max/awesome-bio-agent-skills --skill claw-metagenomics --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.
# 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. Calculates **alpha diversity metrics** from Bracken-adjusted species abundances: - **Shannon diversity index**: H = -sum(p_i * ln(p_i)), where p_i is the proportion of classified reads assigned to species i - **Simpson diversity index**: D = 1 - sum(p_i^2) - **Pielou evenness**: J = H / ln(S), where S is the number of species detected - **Species richness**: S = number of distinct species with at least 1 assigned read 8. Generates four publication-quality fi
- What it does
- Why this exists
- Validated On
- WHO-Critical ARG Detection
- Usage
- Demo (works out of the box)
- Example Output
- Pipeline Architecture
- Database Requirements
- Citations
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
What does the claw-metagenomics skill do?
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill claw-metagenomics --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.