Is there a SILVA database version with only prokaryotes?

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19 months ago

SushiRoll ▴ 140

Hi all!

I was wondering if there was a version of the SILVA database with just prokaryotic sequences? I'm using the last available version (138.1) of the SSU NR99. Indexing takes forever and I realise there are a lot of eukaryotic sequences which I don't really care for in my analysis, I was thinking a purely prokaryotic version would somehow decrease the indexing time.

Thanks!

taxonomy SILVA 16S • 703 views

ADD COMMENT • link 19 months ago by SushiRoll ▴ 140

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Keep in mind that you can still get 16S amplicons from Chloroplast and Mitochondria

ADD REPLY • link 19 months ago by andres.firrincieli 3.8k

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Hi Andres,

Thanks for your reply. To be honest, it doen't technically bother me the presence or absence of non-prokaryotic sequences, my problem is that the indexing takes too long. I'm working through an SSH client and the network gets closed after a while because of this and the indexing can never end.

ADD REPLY • link 19 months ago by SushiRoll ▴ 140

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