I'm sorry if this is post is an extension/copy of others, I've read the other Sanger amplicon related posts but to this specific process I'ven't found something practical.
So, simultaneously with the 16s metataxonomic sequencing (Illumina, Miseq), my team took an culturomic approach over the same pool of samples as the ones sequenced, resulting in a set of sanger amplicons belonging to strains isolated. This set of amplicons sequenced the 8F-907R region and the metataxonomic data sequenced the 385F-805R region, so hipothetically ASV range is contained in the amplicons from culturomics.
Sanger data was first basecalled using Tracy, then trimmed with Cutadapt, then I imported them to q2, dereplicate them using VSEARCH (as suggested in other posts) and assigned taxonomic with the NB classifier. After checking the taxonomy I saw full correspondence between isolated and ASVs taxonomy (yay!).
Now, I'm trying to retrieve the ASVs that might belong to the isolates or be closely related in order to determine how efficient was the culturomics (kinda when an article says "15% of bacteria found in common by metagenomics and culturomics").
At first, I tried a blast search, but the issue with this method is that I only obtain how much of a sequence is shared (in the form of a identity percentage) and that doesn't necessarily answer to other criteria such as a phylogenetic one and as amplicons have regions completely equal that also mess up the blast searches.
I tried clustering the 16s sanger amplicons but that led to nowhere, I tried SEPP but I just got errors and zero phylogenies (apparently it's not designed for Sanger sequences, I don't know what I was expecting tbh). And I haven't add the sanger amplicons to my reference database (SILVA) as the taxonomy of this amplicons isn't clear and I don't want to bug the classifier with fuzzy points. So now I'm trying to determine a straigthforward and painless method to perform this analysis. That's the reason of this post.
So, forum members, what kind of methods would you recommend to perform this kind of search?