🦠 Amplicon 16S

qiime2.sh

• Preprocess
• Quality control & filtering
• Assign taxonomy
• Diversity analysis
• Phylogenetic tree

Create visualizations

R - qiimer2, phyloseq & metagenomeSeq

• Sample composition plots
• Alpha & Beta diversity
• Differential abundance analysis (for zero inflated data)

Python - Microbiome gene set enrichment

• Microbiome set enrichment analysis with MSEA
• Pathways enrichment analysis with GSEApy