Best reference database for 16S soil datasets?

Question

[Lina F]

Hi all,

I came across some interesting 16S datasets from soil. Can anyone recommend a good reference database? RDP vs Silva? The Greengenes webpage highlights the update from May 2013... so maybe a bit outdated.

Thanks for your suggestions!

Answer 1

[5heikki]

RDP and Silva are both fine. Silva is more restrictive in terms of its licence but it's fine for academic use..

[Lina F]

Great, I appreciate the input!!

Answer 2

[Denise CS]

May be worth throwing the EMBL-EBI metagenomics in the comparison mix. No issues with license.

[Lina F]

Thanks for the link! However, these look like metagenomics samples, not necessarily reference databases for use in annotation taxonomies, or am I missing something?