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micom-dev / databases

Workflows and input data for the construction of the standard MICOM model databases.
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SILVA inputs problem with Escherichia and Shigella #1

Open jjoropezav opened 1 year ago

jjoropezav commented 1 year ago

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.

cdiener commented 1 year ago

Yeah, good point. All the databases are built on top of a specific taxonomic naming scheme, and you will get the best results if you match your data to it. Default AGORA uses refseq, so you need the NCBI taxonomy. We built a genus-level classifier based on that for a course. Or you could use the GTDB classifier and use the database versions using that scheme.