Should Deepurify be run with all MAGs from the same dataset?

[kazumaxneo]

Hi,

From the paper, I understand that Deepurify not only removes contaminated contigs but can also reassign contigs between bins or reconstruct new MAGs from a highly contaminated one.
Does this mean it’s recommended to include all MAGs from the same metagenomic dataset as input, rather than only the contaminated ones?

Thanks for your great tool.

Best,
Kazuma

[zoubohao]

Yes, you can input all MAGs into deepurify to reduce the contamination in them. You can also input the fasta and BAM files into deepurify to do iterative binning and decontamination.