Introduction
Requirements
1. Importing data
1.1. Feature tables
1.2. Taxonomy information
1.3. Phylogenetic tree
1.4. Metadata
2. Removing rare taxa and rarefying
2.1. Removing rare taxa
Remembering that some of the workflows already have something for this, so if none are removed then this is fine.
2.2. Looking at rarefaction curves to determine appropriate minimum sampling depth
2.3. Repeated rarefaction
2.4. Other normalisation?
3. Visualising an overview of samples
3.1. Stacked barplots
3.2. Heatmaps
3.3. Combining heatmaps with phylogenetic tree
4. Alpha diversity
4.1. Calculating alpha diversity (on all repeated rarefactions)
Simpson, Shannon, Simpson’s evenness, Faith’s phylogenetic diversity, Chao1, number of taxa
4.2. Visualising alpha diversity
4.3. Stats tests
ANOVA with maybe two variables?
5. Beta diversity
5.1. Calculating beta diversity
Bray-Curtis, Weighted UniFrac, Robust Aitchison’s, phylogenetic PCA?
5.2. Visualising beta diversity
5.3. Stats tests
PERMANOVA, ANOSIM, BETADISPER?
6. Differential abundance
With MaAsLin 3
7. Other interesting methods to check out
Authors: Abbey Saunders
First created: 16 October 2026
Last updated: 16 October 2026
Based on initial versions by: NA
