I am pretty new to bioinformatics and I recently started working on a pipeline for NGS 16S data anysis using qiime2 with a small “get-out, get back in” in that I’m using the Kraken classifier for the taxonomic assignment.
One of my coworker which is doing Sanger 16S was interested and asked if I could add an option for him to identify his sequences, I tried to assemble his 16S sequences (multiple primers to get overlapping sequences) and most of the time they assemble well into a single contig (i’m using cap3 for this task) and by feeding this sequence to a classifier I’m able to get a taxa name for the contig(s). However he also wants a phylogenetic tree like what blast provides.
So my question is basically, instead of using a classifier like Kraken, Centrifuge, SK-learn can I simply blast the sequence against a 16S database and build a phylogenetic tree using the top N results before looking at the taxonomic assignment of the closest sequence(s) in said tree (and return the parent in case of multiple taxa) ? This would give me both the taxonomic and phylogeny informations.
I feel like I’m missing something very important about the difference between Blast and taxonomy classifiers because I only remember people using classifiers to get the taxonomy and not blast, plus the majority of papers and tutorials I’ve read about 16S data analysis only do phylogenetic trees on the OTUs/ASV between themselves.