I am now working on communities of soil and my target genes are 16S, ITS and COI. I have no problems to assign taxonomy to the first 2 taxonomic groups using Greengenes and UNITE (fasta and taxonomy files). however, the BOLD db is not very helpful in assigning taxonomy as most of my species don’t match the DB. for this reason, I am blasting against the NT database of blast. Is anybody aware of the existence of a taxonomy file for that database?
I am not aware of any type of taxonomy file for that database — I believe others may have discussed this elsewhere on this forum, but as far as I know you will need to concoct a script to grab the taxonomy annotations from the fasta header lines and reformat to be qiime-compatible (sounds like you are already using greengenes and unite in QIIME2, so just follow the format of those taxonomy files).
Sorry I don’t have a more satisfying answer! Others may know, or may have already constructed a qiime-compatible taxonomy file for COI sequences — let’s see what others have to say!
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