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micom-dev / databases

Workflows and input data for the construction of the standard MICOM model databases.
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Information on Gapseq models #4

Open anubhavdas0907 opened 3 months ago

anubhavdas0907 commented 3 months ago

Hello Christian,

I was looking into the species level models "uhgg201_refseq216_species_1.qza".

It is mentioned that these were generated using gapseq.

I am assuming, you used the genomes from MGnify. Is it true?

Can you please provide details on the the gapseq parameters you used to generate these models?

Thanks

Anubhav

cdiener commented 3 months ago

Sorry about that. I should have provided more info here. Yes those were models from MGnify, specifically the UHGG subset (version 2.01). The pipeline used to build the models can be found here using GAPSEQ with the docker container from here. The models were all gapfilled on the gut medium provided with GAPSEQ. The specific list of used MGnify assemblies can be found in the database manifest.

anubhavdas0907 commented 3 months ago

Thanks, Christian.

That was very helpful.