I've been looking at various analysis strategies for microbiome and/or metagenome datasets. So far, my very basic understanding points to two common analyses:
- phylogenetic analysis based on 16s RNA sequences
- functional enrichment analysis based on SEED functional annotations
Are there other basic analyses that are part of the "standard" workflow? I'm thinking of the equivalent of RMA --> hierarchical clustering --> ANOVA --> FDR --> GSEA in basic exploratory analysis of microarray data...
Bonus question: Is it correct to say that annotation of these microbial genes is very incomplete at the moment? To my untrained eye, it seems like SEED is the most commonly used resource for annotations, but I can't imagine that scaling with the explosion in microbial sequences, right?