I’m currently trying to classify a dataset using classify-consensus-blast. Though blast refers to the algorithm, not the data source, I actually want to compare my sample sequences against the BLAST offline database. I previously used Greengenes but am looking for an alternative.
The nt and 16s microbial databases from NCBI are saved to my computer, but I’m not sure how to import these into Qiime2 in an appropriate format for the classification (reference reads as FeatureData[Sequence] and taxonomy as FeatureData[Taxonomy]). None of the import formats covered in the tutorial match, and I’m not sure if NCBI data is one of the formats indicated under “Other data types.”
Sorry, these are BLAST-specific formats so I do not know how to convert these! You should check out the BLAST manual to see if there is any way to convert these to FASTA. Otherwise, I believe it is possible to directly download from NCBI nucleotide in FASTA format.