Set of commands to perform denoising, dereplication, and OTU clustering

[JIMR99 (Jose Mendez)]

Hi everyone, could you help me find a set of commands to perform denoising, dereplication, and OTU clustering in Qiime2?
I have qiime2-2020.11 and when I type qiime vsearch to see options, it shows some options like cluster-features-closed-references, cluster-features-de-novo, cluster-features-open-reference, dereplicated-sequences, etc. I have already imported the data to QIIME and understand how to analyze it in DADA2, but for some reason, I am having difficulty finding the commands to perform denoising and subsequent clustering into 97% OTUs.

[Micro_Biologist (Jono Warren)]

If you really want to use OTUs then here is a tutorial to base your analysis from. You would be best off using the outputs from dada2 as your dereplicated sequences and table as this way your dereplication and denoising is already done.

However, why do you want to use OTUs over the ASVs you already have?

[JIMR99 (Jose Mendez)]

Hello! Thank you very much for providing me with valuable information in the tutorial you shared with me. I am currently reviewing it carefully. Regarding the topic of why to choose the use of OTUs instead of ASVs, I must mention that my interest lies in determining which of the two methods will provide me with more accurate results in evaluating the abundances of taxa in model systems, where I know the exact proportion of each of them. In this way, I will be able to determine which of the two methods is more suitable for the specific objectives of my research.