YuliaNuzhnenko Agent Skill: QIIME2 16S Microbiome & Dysbiosis Skill
📌 Description
DADA2 amplicon sequence variant (ASV) dereplication, Alpha/Beta diversity index calculation, SILVA taxonomy classification, and 3D PCoA projections.
🤖 Agent Execution Protocol
When an AI Agent is tasked with qiime2-16s-microbiome:
- Input Validation: Verify that the required input files or coordinates are supplied.
- Environment Check: Ensure dependencies (
QIIME2, DADA2, scikit-bio, phyloseq) are installed. - Execution: Run the protocol pipeline snippet below.
- Output Generation: Produce actionable Markdown/JSON summaries with publication figures.
💻 Protocol Code Snippet
# QIIME2 Diversity Protocol
qiime diversity core-metrics-phylogenetic --i-phylogeny tree.qza --i-table table.qza --p-sampling-depth 10000 --output-dir core-metrics-results
📥 Input & Output Specifications
Input Contract
- Target Files: Valid input data matching domain formats.
- Parameters: Quality thresholds and cutoffs.
Output Contract
- Results Table: Structured summary dataframe or matrix.
- Visualization: Rendered SVG/PNG figures.
📄 License
Distributed under the MIT License. See LICENSE for details.