There are some great tools for 16S datasets, depending on whether you're looking for ASV-level results (dada2: https://benjjneb.github.io/dada2/tutorial_1_8.html) or OTU-level results (mothur: https://mothur.org/wiki/miseq_sop/).I recommend reading about these to see which one best suits your needs. Both of these tools will create an object that will tell you which sequences are in which samples, and an object that will tell you the taxonomy of the sequences. These objects, and your metadata object/csv file, can be used in downstream diversity analyses with R packages suited for 16S data. These packages include phyloseq, vegan, and microviz. Here are two more links which may be useful: https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/set-up-and-pre-processing.html#otu-or-asvs-or-sotus

https://www.nicholas-ollberding.com/post/introduction-to-the-statistical-analysis-of-microbiome-data-in-r/