I got this weird alpha rarefaction curves when I ran it at a sequencing depth of 500, could anyone help me troubleshoot this? Can I go with this, or should I increase the depth?
Hi @Shreeya_qiime and welcome to the :qiime2: forum!
It looks like Shannon values are declining, likely because as the sequencing depth increases, you're averaging over fewer samples (those with lower depth than the sequencing depth are excluded). You may want to generate curves by sample instead of aggregating them by metadata.
We addressed a similar issue recently, and in that case I redirected the user here.
Hope that helps,
Sergio
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