ngs-shotgun-metagenomics Skill
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN. Published by openai in plugins.
What is ngs-shotgun-metagenomics Skill?
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN. Published by openai in plugins. This profile combines repository metadata with install, compatibility, and usage signals so developers can quickly decide whether it fits their agent workflow before opening the source repository.
Automated repository signals based on public metadata such as recency, license, installation evidence, and adoption. These are not a security audit or endorsement.
Key capabilities
- Includes SKILL.md support
- Reusable instructions support
- Database workflows
- Data analysis
- Database workflows use cases
- Data analysis use cases
Technical details
- Install or run with Copy skill directory
When to use ngs-shotgun-metagenomics Skill
- Use it for database workflows.
- Use it for data analysis.
Built with
Editorial notes
Source
- Creator: openai
- Repository: openai/plugins
- Skill file: plugins/ngs-analysis/skills/ngs-shotgun-metagenomics/SKILL.md
What it does
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.
Skill instructions
Shotgun Metagenomics Use this skill for shotgun metagenomic FASTQs. Essential Inputs Confirm: - paired-end or single-end reads - host organism and host-depletion requirement - target outputs: taxonomic profile, functional profile, assembly, binning, or QC only - preferred database family, if any - database paths or permission to download large databases - sample metadata, batches, and negative controls Public Defaults Prefer nf-core/taxprofiler for reproducible taxonomic profiling. Use direct Kraken2/Bracken, MetaPhlAn, or HUMAnN when the user wants a focused path or already has databases installed. For direct backend execution, prefer the plugin runner over handwritten shell when possible because it validates database bundle contents and records resources/resourceplan.json, resourcemanifest.tsv, resourceenv.sh, and resourcereadiness.md. --run-bracken and --run-humann make those database bundles blocking, not merely optional. Preflight bash python plugins/ngs-analysis/scripts/ngsprefli
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Frequently asked questions
What is ngs-shotgun-metagenomics?
ngs-shotgun-metagenomics is a open-source AI agent skill with Copy skill directory. Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.
Who is ngs-shotgun-metagenomics best for?
ngs-shotgun-metagenomics is best for reusing agent instructions, scripts, and references, database workflows, data analysis workflows.
How do I install ngs-shotgun-metagenomics?
Install or run ngs-shotgun-metagenomics using Copy skill directory. Check ngs-shotgun-metagenomics for the latest setup command.
Is ngs-shotgun-metagenomics actively maintained?
ngs-shotgun-metagenomics may need a closer maintenance check before production use.
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