Missing SILVA file in tutorial, step 11

[montoyah]

Hi,

Thank you very much for putting together this tutorial/workflow. Is very helpful!

Where can I get the SILVA files (align and tax) required for step 11?

Thanks,

Oscar.

[rprops]

Hi Oscar,
You can find those here: https://www.mothur.org/wiki/Silva_reference_files#Release_132
In addition, please use the full fasta database for classification instead of the .align fasta in that step. This is more accurate.

Also, the code here is fairly old and tailored towards how I ran it on our HPC, so you may need to change several things for getting it to work on your HPC.

Best of luck,,
Ruben

[montoyah]

Hi Ruben,

Thanks for your quick reply and for the advice.

Could you point out what aspects I should change? I could submit a pull request with updated code/commands if that's okay.

Oscar.

[rprops]

template=silva.nr_v123.align
should be replaced by the complete database fasta that you can download from the link. The .align file is used for alignment only.

Okay to send pull request with changes/updated commands. Appreciate it.

Ruben

[montoyah]

Ruben,

There is no .fasta file in Mothur's Silva.nr_v132.tgz file. It contains a .align and .tax file, thus I couldn't add the improvement recommended by you. Thanks!