I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created.
From visual inspection with IGV, a significant number of both SNPs and SVs appear to be present, but an assembly built entirely from my own sequencing data is not high enough quality for my purposes.
How can I modify this reference genome to match my sample with new sequencing data (preferably with Oxford Nanopore Technologies long reads, but I can also use these to scaffold short reads if necessary), taking advantage of my knowledge that the existing reference is mostly very good, without having to access the reads which were originally used to construct the reference genome?