domains / families / science / bio-microbiome-qiime2-workflow

bio-microbiome-qiime2-workflow

separate

QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.

When to use

• 16S/ITS amplicon analysis
• QIIME2 CLI workflow
• Denoising with DADA2 or Deblur
• Taxonomy assignment
• Phylogenetic tree construction
• Diversity analysis
• Differential abundance (ANCOM)
• Export to R/Python

When not to use

• DADA2/phyloseq R workflow

Skill page

Source