Performance and running time of classify-consensus-blast+

[Nicholas_Bokulich]

Hi @steff1088,
Your workflow looks correct to me; there is also a community tutorial on OTU picking here that may be useful in case you have not already seen it.

@steff1088

I am running subsets to test the workflow first

@steff1088

Could I theoretically use taxa barplot here already along with SILVA’s otu.qza as taxonomy file?

I think not, since this is open reference and many of the OTUs will have no associated SILVA ID/taxon. If you used closed reference, that should be possible.

@steff1088

Then, I reformatted this file (.tsv) and used it as input for the qiime feature-table filter-seqs command resulting in a filtered sequence file

You are using the currently recommended workaround but just FYI soon that feature table could be passed to filter-seqs directly. See this issue to track progress.

@steff1088

Here I used for both commands the clustered table and sequence file from the open-reference clustering, is that right?

correct

@steff1088

As reference read inputs I used the otu.qza file as in the cluster step.

Yes, as long as these OTUs correspond to the 16Sonly_consensus_taxonomy_7_levels.qza.

@steff1088

To move on, I would basically use the output taxonomy and the filtered feature table file to make taxa barplot, correct?

Correct! and all other downstream analyses.

I hope that helps! Let us know if you run into any trouble (probably in a separate thread).

Happy QIIMEing