Individual skill
microbiome-analysis
16S and microbiome data analysis — denoising, diversity, differential abundance, and compositional methods.
skills/microbiome-analysis/SKILL.md
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## Overview
microbiome-analysis covers marker-gene (16S/ITS) and general microbiome data analysis:
denoising to ASVs, taxonomic assignment, diversity analysis (alpha/beta), differential
abundance with compositional methods, and linking microbiome to host phenotypes. For shotgun
metagenomics, see metagenomics — this skill focuses on the amplicon workflow and the
statistical principles shared across microbiome data types.
## When to use
- 16S experimental design: variable region, controls, sequencing depth.
- Denoising: DADA2 (ASVs) vs OTU clustering — and why ASVs won.
- Taxonomic assignment: SILVA, Greengenes2, RDP — database choice.
- Alpha diversity: Shannon, Faith's PD, observed ASVs — and rarefaction debates.