Silva database for qiime

[Vasily Tokarev]

Hello everyone,

I want to use SILVA database for 18s. I am trying to find out what files do I need to use as a reference in identify_chimeric_seqs.py using usearch61 and what should I use in assign_taxonomy.py for -t and -r.

I will appreciate any help, especially if the answer will have a link to download the files I need :)

Thank you,

Vasily Tokarev

[Jose Navas]

Hi Vasilky,

In this page you have links for the Silva DB (among other QIIME useful links). The specific files for -t and -r depends on the % similarity that you want to use, but the files for -r are under the rep_set folder and the files for -t under the taxonomy folder.

Cheers,

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Jose Navas

[Vasily Tokarev]

Hi Jose,

Thank you for your answer but I have seen that link. There are 2 releases for 119 version. Silva_119_provisional_release.zip looks like what I need. However, what is the purpose of Silva_119_release_aligned_rep_files.tar.gz then?

Best,

Vasily Tokarev

[Tony Walters]

Vasily, the aligned rep files are in case someone wanted to build trees from the alignments with their own software, and aren't generally needed for analyses.

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[Vasily Tokarev]

Also, what file should use as a reference for identify_chimeric_seqs?

[Tony Walters]

You would use the rep set files, e.g. the 97% OTUs.

On Wed, Jul 1, 2015 at 4:30 PM, Vasily Tokarev <tokarev...@gmail.com> wrote:

Also, what file should use as a reference for identify_chimeric_seqs?

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[Vasily Tokarev]

Oh, makes sense, thank you! I still have one more question though.

[Vasily Tokarev]

Ok, thanks a lot everyone!