Do you mean genetic region or geographic region?

Yes, please clarify regarding Urban Olsson 's question.

It sounds like you are at the very beginning stage of analysis where you have .fasta or .fastq files?

If this is the case, the next step is to process them using a bioinformatics tool that can trim, quality-filter, etc. either, for OTU-based analysis, using mothur or QIIME (I am particularly fond of mothur, although this is a continuous debate in the field), or for ASV-based analysis using DADA2.

Urban Olsson of a geographical region

You can have a look at this material that uses R.

https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/alpha-diversities.html