Shannon index decomposition into phylum, class, order, family, genus, species


I am new to doing bioinformatics and I am processing my 16S data. I was already able to produce some alpha diversity graphs with the microbiome analyst package using my ASV final files (.shared and .taxonomy). However, I am now interested in building a table that has the Shannon Diversity index to phylum, class, order, etc. to see which of my treatments have more diversity per taxonomy level. Does anyone have some links on what command or a hint in the sequence of code I can look into to achieve this?

Thank you!

Never tried to implement something like his but in theory one achieve such goal following next steps:

  1. Collapse feature table to desired taxonomy levels
  2. Run core-metrics non-phylogenetic with collapsed tables to get shannon indices, or use collapsed tables with microbiome analyst package.
1 Like

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