Hi, I downloaded the 16S refseqs database from NCBI for taxonomic assignment, along with the corresponding taxonomy using Entrez from the command line. However, when I checked the Taxonomy file, not all records had 7 levels, for instance, any record from the phylum Actinobacteria only has 6 levels,…

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 seam…

That was freaking amazing!!! :sunglasses: It took like 5 minutes to do what I've been trying to do for the past four days with Entrez. Thank you very much for this!!! I know you have done an extensive overview of the functions of RESCRIPt regarding the SILVA database, but I hope in the future a l…

Thanks @ancazugo ! Glad to hear RESCRIPt was useful to you! :smile: [image] ancazugo: I know you have done an extensive overview of the functions of RESCRIPt regarding the SILVA database, but I hope in the future a little tutorial on the use of NCBI is available; nevertheless, it is pretty strai…

mini-update: I just added a tutorial for the get-ncbi-data method here: [image] Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank Tutorials This tutorial will describe how to create custom reference databases from NCBI Genb…

Taxonomy Levels from NCBI custom Database

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Nicholas_Bokulich (Nicholas Bokulich) August 4, 2020, 3:39pm 5

mini-update: I just added a tutorial for the get-ncbi-data method here:

Thanks @ancazugo!