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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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link to kegg database #824

Closed bresyd closed 2 months ago

bresyd commented 2 months ago

Hi,

I am currently preparing the final submission of a paper for which I have used the SQM pipeline. I was contacted by the journal that I need to provide links to all databases that were used during the anlysis in a reporting summary document. For nr, eggnog and pfam I found links to download the respective databases. However, I can not find the kegg database v58 anywhere to download. So I wanted to ask if you guys maybe had a link available that points to this database, and that I can include in the reporting summary?

Thanks a lot for your help

fpusan commented 2 months ago

We host it ourselves. http://andes.cnb.csic.es/SqueezeMeta/kegg.db.gz http://silvani.cnb.csic.es/SqueezeMeta/kegg.db.gz Pretty sure it is ok to include it in your submission. Not fully sure it is version 58 though, @jtamames can you confirm this?

jtamames commented 2 months ago

KEGG requires a licensing, so we are using the last public version released, which I think it was 58. If I remember correctly, that corresponds to 2011.

bresyd commented 2 months ago

Hi Fernando and Javier,

thanks a lot for both of your replies and for allowing to use one of the above links, that should certainly meet the requirements I was asked for.

As always, your support for SQM is outstanding.

Cheers