MOTHUR for microbiome species composition profiling

Respected users,
I have a bunch of files for metagenomic 16S rRNA gene sequences. I want to do species composition profiling from those sequences using MOTHUR. can you please tell me in short what steps should I follow for that?
I just want to know which species and strains are there and their abundances as well.

When you say “metagenomic 16S rRNA gene sequences” do you mean amplicons? Currently the term metagenomic is used to described the sequencing of all potential genes in a sample including 16S rRNA genes, where as amplicon sequencing indicates that you used primers to amplify a specific region of the 16S rRNA gene.

Yes Sir. I am talking about amplicon.

Okay, in that case you will want to follow the mothur SOP from the start (make.files) to the make.shared or sub.sample commands. Once you have gone through all these steps you will ultimately have a file with OTUs and abundances per sample and a file with taxonomic classifications assigned to OTUs. You’ll need to use a program like R to get one table with taxonomy, OTUs, and abundances per sample.

Some recommendations:

  1. Go through the SOP slowly. The time you take to understand each step will save you a ton of time in the long run.

  2. Go through the SOP either with the practice dataset provided or with a small subset of your own samples

  3. To learn more about each step open up the wiki for each command in another tab as you are going through the SOP

thanks a lot for your recommendations. I am going through the SOP.

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