How to find shared OTUs between samples?

Dear Friends,

Could you please let me know how to find shared OTUs between samples using QIIME? This analysis will help me in phylogeny interpretation. Thank you!

Hi @danielsebas,
QIIME 2 does not have a method that will explicitly tell you the number of shared OTUs, but you can look at Jaccard distance (one of the outputs of qiime diversity core-metrics), which tells you the fraction of observations that are NOT shared between each pair of samples, so is effectively the inverse of shared OTUs.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.