Hello! I have a pretty broad question about qiime2 fragment-insertion, and apologies if this has been discussed previously.
I am interested in inserting short reads analyzed with dada2 and deblur into small curated reference phylogenies, like a few hundred sequences. for one project I am working with really low diversity datasets, and really only have one ASV per sample which I am adding to the phylogeny. For another project I am working with datasets with normal diversity but am focused on seqeunces which are more rare, generally 0-10% of the total reads. I like fragment-insertion because I can analyze reads from different primer sets together, and because it can generate new branches on the tree, not just add to existing branches.
I have tried this and gotten it to work successfully with my own reference dataset(s). But i have gotten some funky results that disagree with multiple other methods I have used (de novo phylogeny, taxonomic assignment, and full length sanger sequencing of the same population for the low diversity data, etc.)
My questions are: Is the actualy phylogenetic tree that you get as output reasonably reliable? Or should it really only be used for downstream analyses and not visualized on its own? are the phylogenetic relationships between the inserted seqeunces reliable?