Hi there! I have some doubts about taxonomical asignment.
The pre-formatted SILVA reference sequence and taxonomy files that can be found in Data resources — QIIME 2 2020.6.0 documentation contain both 16S and 18S SSU references, right?
Is there any way I can choose using only 16S references?
Another question I have is, are there any resources available for PR2 to use with BLAST classification on Qiime2 like the SILVA reference sequences and associated taxonomy files ?
One last doubt is about doing the taxonomical asignment using vsearch vs BLAST. I’ve tried them both with a set of 12 samples and while the process with vsearch lasted ~ 38h, with BLAST it took just 1 hour. Is this explained by the fact that in vsearch global alignments are made while in vsearch they are local?
Thanks you so much!