--p-perc-identity meaning

[dafneposa]

Hello!

I am working with 16S gene sequences in a metagenomics study. I was wondering what --p-perc-identity in "qiime feature-classifier classify-consensus-blast" means. If I set a --p-perc-identity 0.97 value, but an ASV is only classified at phylum level, what does it mean? To consider two different sequences within the same phylum only a 0.7 percentaje identiity is needed, but if 0.97 is setted, I don't undesrtand how the taxonomical truncation is made. Is there any consensus sequence in the database at phylum level and the --p-perc-identity 0.97 is compared against that one?

I hope you can help me, thank you in advance.

[colinbrislawn (Colin J Brislawn)]

@dafneposa

I was wondering what --p-perc-identity in "qiime feature-classifier classify-consensus-blast" means.

Here's the documentation for qiime feature-classifier classify-consensus-blast.

Note that this threshold of 0.8 is much lower than the 0.97 or 0.99 used for OTU clustering. Do you see why that works well for blast consensus taxonomy, where we would want a much higher threshold for clustering?