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qiime2-microbiome-analyzer

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QIIME2 microbiome analysis skill for 16S rRNA profiling and diversity analysis

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Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/qiime2-microbiome-analyzer/SKILL.md

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QIIME2 Microbiome Analyzer Skill

Purpose

Enable QIIME2 microbiome analysis for 16S rRNA profiling and diversity analysis.

Capabilities

  • Demultiplexing and denoising (DADA2)
  • Taxonomic classification
  • Alpha diversity metrics
  • Beta diversity analysis
  • Differential abundance testing
  • Phylogenetic analysis

Usage Guidelines

  • Use DADA2 for denoising amplicon data
  • Select appropriate taxonomic classifier
  • Calculate diversity metrics with rarefaction
  • Visualize beta diversity with ordination
  • Test differential abundance appropriately
  • Document pipeline parameters

Dependencies

  • QIIME2
  • DADA2
  • phyloseq

Process Integration

  • 16S rRNA Microbiome Analysis (16s-microbiome-analysis)