VGP decontamination

Hello VGP mentors,

I was following the VGP assembly pipeline to assemble my newly sequenced genome, which is a big convinence for someone like me who didn’t have a lot of bioinformatics experience. However, I found there is supposed to be a decontamination step in the VGP workflow, while it’s not avaliable in the tutorial. Will there be an update for the decontamination step? It would be very helpful for my genome which contains microbial contaminations naturally. Thank you very much!

Zi Ye


Thank you for your feedback!
We don’t have a tutorial for the decontamination step but you can find the workflow here: Dockstore.
The inputs are simply your assembled genome and the database you want to use to decontaminate your assembly.




Thank you very much for your reply and workflow!
Best regards,
Zi Ye