We asked a company to run NGS for an unknown purified virus but the result looks really strange after alignment and BLAST.
We think our virus is a begomovirus. These viruses sometimes have two circular DNA genome (bi-partite), and sometimes just one genome (mono-partite). We think the weird sequence could be because the company aligned the results against a mono-partite genome, but we're not sure. Some part of the sequence they gave us matches begomoviruses, but the other parts match with rat and other species!!!
We asked the company to give us raw data so we can align it ourselves, but I'm not really good with the software and reading of raw data, so I'm not sure what do to if we have a bi-partite genome.
Maybe I just add the sequence of the second genome to the first genome and align? But does bi-partite genome affect NGS reading in first place?