I am writing about classify-consensus-blast. I am trying to simply blast(n), but NOT assign taxonomy. Taxonomy is a required field, so rather than create a standin taxonomy to fit the requirements, is there some other way I am missing in qiime2 to directly blastn against a database (.fasta)?
Thank you very much!
Hello again @camzdel,
This is possible but just to give an initial disclaimer — this method was specifically designed to assign taxonomy and is not just blastn. The q2-feature-classifier method uses blastn for alignment, then q2-feature-classifier takes that output, looks up the taxonomy of all hits, and attempts to find a consensus taxonomy among them. So if you just want blastn, it might make more sense to just use blastn directly.
That taxonomy could be any kind of annotation. So it could map to gene names, feature IDs, or any other information.
qiime quality-control evaluate-seqs
That uses blastn for alignment without any additional processing, just creates a visualization of the full blastn report… see the example here: