Hi, I am new to NGS/ genome assembly field. I am given data and assembly (done by someone else) to evaluate if it is correct and if not, do the assembly myself. To check the given draft assembly, I mapped the largest scaffold of the existing reference genome (about 4Mb), using it as query to our draft assembly with blast+ and found that the query scaffold maps to 195 different scaffolds of the draft assembly. 1. I think this means that the assembly is highly fragmented?
The person is justifying this by saying that it is due to the presence of several gaps (Ns) in the query scaffold. Can someone please shed some light on this matter?