Purging step in VGP removing bacterial symbiont from genome


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 ?



The purging step may be removing bacterial DNA if the coverage is too high. You can get the purged sequences from the purgedups workflow (dataset tagged with “seq_purged_p2”) if you want to collect the bacterial DNA that has been purged. In addition to using the decontamination workflow after scaffolding you should be able to recover all the data from the symbiont.

I hope it helps,


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