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

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1

I am using qiime2 2022.8
How is the "consensus" calculated in qiime feature-classifier classify-consensus-blast? It is crucial to me for understanding how to parametrize this tool.

2

I agree!

Let's start here, with the documentation for classify-consensus-blast.

Performs BLAST+ local
alignment between query and reference_reads, then assigns consensus taxonomy
to each query sequence from among maxaccepts hits, min_consensus of which
share that taxonomic assignment. Note that maxaccepts selects the first N
hits with > perc_identity similarity to query

--p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False,
inclusive_end=True) Minimum fraction of assignments must match top hit
to be accepted as consensus assignment.
[default: 0.51]

For even more details and technical notes on the implementation, here's the code.

3

Thanks for the answer. I think that apart of providing the code, the process of the consensus is not clear to me. For each esv there is a taxonomic assignment and a value. What is this value exactly?
Moreover, if I set a perc identity of 98 which yields:
id A perc 98.3, id A perc 98.4, id B 99.9.
Will I get id B because higher id perc or A because of majority of cases?
I also looked at the citation given by --citation but there is nothing about consensus there (=wrong citation)...

5

The citation for consensus is part of the feature classifier:
qiime feature-classifier --citations

All three of those will be accepted because they are over your threshold, and the taxonomy level that agrees >51% of the time across those three will be selected.

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6

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

8

Thank you for your patience.

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.

11

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