Modify Scaffolds to create a New reference

Question

[ben.blais]

Hello everyone, I would like to ask you about a current problem which I face. Indeed, I got scaffolds from contigs. Then, I used Blat to compare these scaffolds to a near reference, and then visualize this alignment with IGV. When viewing, I can see that there are small gaps when aligning the scaffolds on the reference. I would like to know if it is possible to modify these scaffolds and thus to fill the gaps by N in order to create a "new reference"? I hope I have been pretty clear in my comments. Thanks you in advance for any help and wish you an excellent end of the day.

[h.mon]

There is a good number of publications for reference-based scaffolding, e.g.:

https://www.ncbi.nlm.nih.gov/pubmed/30598087

https://www.ncbi.nlm.nih.gov/pubmed/27549770

https://www.ncbi.nlm.nih.gov/pubmed/23307812

https://www.ncbi.nlm.nih.gov/pubmed/19497936