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philarevalo / PopCOGenT

Microbial Populations as Clusters Of Gene Transfer
GNU General Public License v3.0
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Is it acceptable to work with MAGs? #26

Open sarpiens opened 2 years ago

sarpiens commented 2 years ago

Hello,

I have recently read your article regarding your tool and find it very interesting. However, I have a doubt regarding the expected inputs, because in the publication it is mentioned mostly applied to SAGs or even genomes from single cell. I wonder if it would be acceptable to also introduce MAGs in the analysis, since MAGs themself would be a set of population genomes? And if so, which ones would be acceptable, since in general there are those who work with medium quality MAGs (completeness estimates of ≥50% and less than 10% contamination), and others who work only with high quality MAGs (>90% complete with less than 5% contamination)?

philarevalo commented 2 years ago

At the time of publication, we had not tested this method with MAGs and did not have good intuition for how contamination might affect the results. Since MAG assembly methods have improved, this might make using MAGs more feasible, but again, it's not something that we have dug into either practically or theoretically, so I can't recommend it.

sarpiens commented 2 years ago

Okey. Thank you very much for your quick response! Best regards.