metagenomics
Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.
npx skills add BioTender-max/awesome-bio-agent-skills --skill 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.
# Metagenomics ## Version Compatibility Reference examples assume: - `fastp` 0.23+ - `kraken2` 2.1+ - `bracken` 2.8+ - `metaphlan` 4+ - `humann` 3.9+ Verify the environment first: - CLI: `kraken2 --version`, `bracken -v`, `metaphlan --version`, `humann --version` ## Overview Use this skill for shotgun metagenomics when the user needs: - QC and host depletion review - taxonomic abundance tables - functional pathway profiles - AMR or strain-level follow-up ## When To Use This Skill - the data are shotgun metagenomics rather than amplicon sequencing - the user wants species or genus abundances, function, or resistance summaries - multiple samples need cohort-level comparison ## Quick Route - host-associated samples: perform host depletion before interpretation - taxonomy only: `kraken2 + bracken` is a common pragmatic route - function only or plus taxonomy: add `humann` - strain claims require more evidence than top-level taxonomy calls ## Progressive Disclosure - Read [technical_reference.md](technical_reference.md) for database choice, host contamination review, and functional profiling caveats. - Read [commands_and_thresholds.md](commands_and_thresholds.md) for command-line pattern
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Expected Inputs
- Expected Outputs
- Starter Pattern
- Workflow
- 1. Run read QC and optional host depletion
- 2. Profile taxonomy
- 3. Refine abundance tables
- 4. Add function or AMR when requested
- 5. Export cohort-ready outputs
fastp \ kraken2 \
What does the metagenomics skill do?
Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill 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.