Sequence and taxonomy files for Silva v138.2

[Laura_R]

Hello,

I would like to perform taxonomic assignment on samples for which we sequenced the amplicon corresponding to the 18S ribosomal RNA gene (V4 region), using SILVA database version 138.2. However, I’m not sure whether the sequence and taxonomy files for this version are available in the QIIME 2 data resources (Data resources — QIIME 2 2024.10.1 documentation), since only version 138 is listed there. Could you please confirm if those files correspond to version 138.2 or tell me where I can download them directly?

Thank you very much.

[Julio (Jianxujie Zheng)]

Hi Laura_R,

You can see here:
Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt:

@SoilRotifer

Getting SILVA data the easy way

We actually have a nice convenience method to perform all the tasks outlined in the Hard Mode section, using a single command!* Which is… :

qiime rescript get-silva-data \
    --p-version '138.2' \
    --p-target 'SSURef_NR99' \
    --o-silva-sequences silva-138.2-ssu-nr99-rna-seqs.qza \
    --o-silva-taxonomy silva-138.2-ssu-nr99-tax.qza

Best regards,
Julio

[SoilRotifer (Mike Robeson)]

Hi @Laura_R,

If you download the files on that page, you can then use QIIME 2 View, to look at the provenance information. The provenance says 138' not 138.1 or 138.2. I recommend you follow the tutorial that @Julio linked above and construct your own classifier. You can pick the steps you'd like to use during construction.

For example, here is one quick way to make an amplicon specific classifier. Though, I'd likely add the qiime rescript cull-seqs ... after the amplicon extraction step.

If you are unable to build the classifier on your machine, checkout this post.

-Mike