micom-dev / databases Goto Github PK

Hi again @cdiener thank you always for your help, This is not an issue from micom but from the silva and the databases properly.
I ran my simulations with micom and found surprised that the genus escherichia neither shigella grew in my models using AGORA or AGORA2.

Found that the problem is that my qiime artifacts were trained with SILVA, currently SILVA have a new genus established as Escherichia-Shigella.

https://www.biorxiv.org/node/2170154.full
https://www.arb-silva.de/browser/ssu-138/AM184304

i modified the manifest file to correct this, if you want i can send them to you.

Thanks a lot.

Hi Diener,
would it possible to provide detailed description on the procedures that generated those GEM reference database? I found it quite useful while I am hesitating to use it in my manuscript without any description on how those GEM reference database were produced.

many thanks,
Zhaoju