Importing Offline BLAST to Qiime2 Archive

Hi Qiime2 Users,

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.”

Any help would be appreciated!

So NCBI nucleotide database?

To import any reference database, it needs to be in the same format — you can use the tutorial data as a guide.

So sequences need to be in fasta format

Taxonomies need to be in TSV format with semicolon-delimited taxonomy annotations

Let us know if you have any questions!


You are correct, I’m looking to compare the sequences against the NCBI nucleotide database.

The problem I’m having is that the filetypes for the downloaded dataset are .nhr, .nin, .nnd, .nni, .nog, .nsd, .nsi, .nsq, .btd, and .bti. I don’t recognize any of these as importable formats.

Is there a Qiime option that accepts any of these? Alternatively, is it possible to convert the data type?

Thank you!

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.

I’ll review the manual then. Thank you very much!

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