qiime feature-classifier classify-sklearn output with more than one hit per ASV

[CrisZ (Cristina Zamora)]

I'm wondering if there is an option together with qiime feature-classifier classify-sklearn for getting more than one hit per ASV in the output table, something similar to --p-maxaccepts when using BLAST.
Thank you!

[Nicholas_Bokulich]

Hi @CrisZ ,
This is an interesting question but the short answer is no. The methods used by this action work quite differently from an alignment-based classfier like BLAST, and do not report hits to individual reference sequences. Instead, they report the probability of belonging to each unique taxonomic group, and a classification is only used if there is a strong probability of belonging to one single group (default confidence = 70%). The raw probabilities are not output, thought technically this would be possible by editing the source code.

If you are looking for a report on similarity to individual reference sequences, the latest release of q2-feature-classifier includes separate blast and vsearch actions that will generate the typical blast6 format "hits" table.