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.:
- alpha rarefaction or beta rarefaction results
- how willing you are to lose particular samples
- how willing you are to compromise regarding coverage vs. depth
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