Which Silva .txt file to use?

Hi all,

I’m currently analyzing some 16S data, and am trying to use Silva to assign taxonomy to my samples. I’ve already downloaded Silva138 as a reference database, and used the following command:

qiime tools import
–type ‘FeatureData[Sequence]’
–input-path /Users/samgoldman/Desktop/SILVA_138_SSURef_NR99_tax_silva.fasta
–output-path /Users/samgoldman/Desktop/SILVA_138_SSURef_NR99_tax_silva.qza

I’m following some old code from a labmate, and she has the following as the next step:

qiime tools import
–type ‘FeatureData[Taxonomy]’
–input-format HeaderlessTSVTaxonomyFormat

I’m on the Silva website trying to download a .txt file to use, but there are a lot of options: https://www.arb-silva.de/no_cache/download/archive/release_138/Exports/taxonomy/

Anyone have any guidelines as to which I should choose?



Hello Sam,

Well, because you have downloaded SILVA_138_SSURef_NR99_tax_silva.fasta, you will want one of the files that’s includes ssu_ref_nr99_138.

But, there are still so many choices! Let’s see if @SoilRotifer can recommend one version over the others.



Hi @slgoldman, welcome to :qiime2:!

I can refer you to our prototype classifiers as outlined here:

There, you will find information about the pipeline (still a work in progress), and the files you need to download.

-Hope this helps!


Thank you both! This was very helpful.

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