I’m interested in calculating the expected amplicon sizes of a primer set targetting V1-2 region of the 16S rRNA. Are the reference sequences extracted from the database by
qiime feature-classifier extract-reads suitable for that purpose? The default minimum combined primer match identity threshold (0.8) is quite lenient compared to what’s usually used in the in silico evaluation of universal primer sets, which allows no or a single non-3′-mismatch.
Any comments or suggestions are welcome.