The following guidelines are based on the excellent paper by Weiss et al on data from 16S data.
- DESeq2 has the highest power to compare groups, especially for less than 20 samples per group.
- MetagenomeSeq’s fitZIG is a faster alternative to DESeq2 for large samples (over 50 samples per group)
- For larger sample sizes (over 50 samples), rarefying paired with a non-parametric test, such as the Mann-Whitney test, can also yield equally high sensitivity.