I'm looking for a code to generate a rarefaction curve showing that our samples have great sequencing depth similar to the figure below. So far, I've found codes for alpha and beta rarefaction curves, which I'm not interested in.
I was thinking of a code similar to the one listed below. However, I don't know what word to fill in the blank. I tried "qiime diversity rarefaction" and it didn't work.
qiime diversity (_____) rarefaction
--o-visualization rarefaction.qzv \
The only rarefaction visualizers we have within the QIIME 2 core distribution are for alpha and beta rarefaction. With that being said, I did a quick search on any other existing rarefaction plots, and it seems like the Rarefaction Tool Kit R Package might be a good option for you to investigate.
Best of luck, hope this helps! Cheers
Thank you for your response! Based on what you said, I have to use r to generate rarefaction plot of ASV and sequencing depth. Is that correct?
So if you're trying to obtain rarefaction curves for observed features (i.e. ASVs), you actually would want to use alpha rarefaction within QIIME 2. My apologies, I wasn't entirely sure what kind of rarefaction plot you were hoping to utilize since you mentioned you weren't interested in alpha or beta rarefaction.
Here's an example visualization of an alpha rarefaction plot from the Moving Pictures tutorial - you can set the metric to 'observed_features' and this should get you what you're looking for (i.e. sequencing depth vs. observed features).
Hope this helps! Cheers
Thank you so much @lizgehret. I was able to generate the plot as you mentioned!
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