Extracting sequence depth information from feature-table QZA file

Is there a way to parse through a QZA file so I can extract information about sequence depth and automate from ASV generation to core diversity analysis?

Hi @ange,
I am not 100% sure this answers your question, but qiime feature-table summarize will give you the information you want — the distribution of sequencing depths for each sample.

Nothing exists to my knowledge (though I have contemplated putting such a method together). It is not a trivial process, though, since so much about that process is subjective because you may make rarefaction and filtering decisions based on multiple criteria, e.g.:

  1. alpha rarefaction or beta rarefaction results
  2. how willing you are to lose particular samples
  3. how willing you are to compromise regarding coverage vs. depth

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