Which Silva .txt file to use?

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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
–input-path
–output-path

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?

Thanks!

Sam

2

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.

Colin

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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!
-Mike

3 Likes
4

Thank you both! This was very helpful.

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