Microbiome Resources
Simulations
CAMISIM: simulating metagenomes and microbial communities is a recent 2019 paper that simulates microbial communities and metagenomes. It was originally created to generate simulated datasets for the first CAMI challenge (Critical Assessment of Metagenome Interpretation).
MetaSim describes a method to simulate individual read datasets for planning out sequencing projects and benchmarking metagenomic analysis software.
SparseDOSSA is a R based tool that can simulate OTU tables that have correlation structure if you want to do some sort of association testing.
Compositional Methods
Compositional Data Analysis in a Nutshell covers the proper mathematical operations for compositional data, including centralized log ratio.
A Concise Guide to Compositional Data Analysis by the man himself John Aitchison - (the Aitchison geometry).
Linear Association in Compositional Data Analysis
Distance Metrics
Compositional Data Analysis (CoDA) Approaches to Distance in Information Retrieval