I am following VGP workflow and have an issue with purging step. I am using purging mainly to decrease the number of contigs i have as when doing direct scaffolding from hifiasm i am ending up with big number of scaffolds.
However, purging step appear to be removing bacterial DNA known to be present present in the sequenced insect chromosome. I also confirmed its presence in the HIFIASM assembly but it get wiped out from the purged assembly.
Kindly, any suggestion how to deal with this as i would like to maintain the bacterial DNA in the resulting purged sequences ?