how is consensus calculated in qiime feature-classifier classify-consensus-blast

[colinbrislawn (Colin J Brislawn)]

Thank you for your patience.

@PB001

And the consensus value given by the function, how is it calculated?

It's the fraction of hits that all list the same taxonomy result.

Paraphrased from this section of the paper:

A consensus taxonomy is then assigned by determining the taxonomic lineage on which at least min_consensus of the aligned sequences agree. This consensus taxonomy is truncated at the taxonomic level at which less than min_consensus of taxonomies agree.

For example, if a query sequence is classified with maxaccepts = 3 and gives these his:
f__Lactobacillaceae; g__Lactobacillus; s__brevis.
f__Lactobacillaceae; g__Lactobacillus; s__brevis.
f__Lactobacillaceae; g__Lactobacillus; s__delbrueckii.
The taxonomy label assigned with min_consensus = 0.51 would be
f__Lactobacillaceae; g__Lactobacillus; s__brevis.
However, if min_consensus = 0.99, the taxonomy would be
f__Lactobacillaceae; g__Lactobacillus.