Taxonomy Levels from NCBI custom Database

[Nicholas_Bokulich]

Hi @ancazugo,
I have good news (or shameless self-promotion, depending on how you see things). We recently released a QIIME 2 plugin, RESCRIPt, that can automate the process of downloading and formatting NCBI Genbank data... using the get-ncbi-data method in RESCRIPt, you can do this much more seamlessly, and will not need to manually format your taxonomy.

@ancazugo

when I checked the Taxonomy file, not all records had 7 levels, for instance, any record from the phylum Actinobacteria only has 6 levels, since Actinobacteria is both the Phylum and the Class, so it is not reported twice in the NCBI lineage. Is this a problem for the training classifier or the taxonomic assignment? or should I fill the missing levels for the incomplete records?

Yes, uneven levels will cause problems downstream with various classification methods. You should either reformat to create even levels, or use RESCRIPt, which will do that automatically.

@ancazugo

Should my custom taxonomy file look like this, with the underscores and D_0, D_1…?

No, that's specific to the database and is not anything special that QIIME 2 requires. That said, having those prefixes can sometimes aid interpretation (e.g., so it is clear what rank a classification was made to).

I hope that helps!