ngs-amplicon-microbiome Skill
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt. Published by openai in plugins.
What is ngs-amplicon-microbiome Skill?
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt. 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-amplicon-microbiome 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-amplicon-microbiome/SKILL.md
What it does
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.
Skill instructions
Amplicon Microbiome Use this skill for marker-gene microbiome analysis from amplicon FASTQs. Essential Inputs Confirm: - marker region: 16S, 18S, ITS, COI, or custom - primer sequences and orientation - paired-end or single-end reads - whether reads should be merged - taxonomy database and version - sample metadata - endpoint: ASV table, taxonomy, diversity, differential abundance, or plots Public Defaults Prefer nf-core/ampliseq for reproducible end-to-end runs. Use QIIME2 or DADA2 directly when the user wants notebook-level control or an existing lab protocol requires it. Preflight bash python plugins/ngs-analysis/scripts/ngspreflight.py --pipeline ampliconmicrobiome --emit-install-plan Local Execution Package For FASTQ intake/QC before primer, ASV, and taxonomy decisions, use: bash python plugins/ngs-analysis/scripts/runfastqassaypackage.py \ --lane ampliconmicrobiome \ --sample-sheet ampliconsamples.tsv \ --execute This validates read paths and structure, runs seqkit stats and Fast
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Frequently asked questions
What is ngs-amplicon-microbiome?
ngs-amplicon-microbiome is a open-source AI agent skill with Copy skill directory. Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.
Who is ngs-amplicon-microbiome best for?
ngs-amplicon-microbiome is best for reusing agent instructions, scripts, and references, database workflows, data analysis workflows.
How do I install ngs-amplicon-microbiome?
Install or run ngs-amplicon-microbiome using Copy skill directory. Check ngs-amplicon-microbiome for the latest setup command.
Is ngs-amplicon-microbiome actively maintained?
ngs-amplicon-microbiome may need a closer maintenance check before production use.
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