Hey everyone, I'm new here, so apologies if my question is broad or a bit obvious. I'm a biotechnology graduate doing an internship for the summer. I have some limited experience in bioinformatics, but I've spent the last month learning QIIME, reading papers and getting a sense of 16s rRNA analysis.

I am looking to create a library of 10 pathogenic bacteria. the aim is to identify with accuracy if the 16S rRNA sample is one of these 10 or not.

I was thinking the best way to do this would be to get 100 sequeneces of each of the species of interest (E. coli, Klebsiella) from SILVA and run a MSA. I've done this with Seaview. From this MSA I would like to create a representative 16s rRNA sequence for each species (think of it as an average of all of them). From the 100 seqs MSA, I was hoping to be able to identify conserved/variable regions for each species, that I can use to accurately identify if the sample contains one of the 10 bacterial species or not.

I was wondering, how best I can go about this. I found this 2012 paper entitled "Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment Nagar et al "

Here, they use some R packages including "Quasi Align". Following the links provided, it shows that these tools were last updated in 2015 and are no longer supported by R.

I then tried to look up more recent papers, but nothing of interest popped up.

I was wondering if you would be so kind as to share your knowledge and give some constructive criticism on shown best to go about this.

In conclusion: I want to identify 16s rRNA conserved and variable regions of 10 different pathogenic bacteria, so I can accurately identify if they are in a sequenced sample or not

Thanks a lot - Rob :)