Custom Genome - How to replace string with a new string based on coordinates

Question

[josephmccarter1]

Hi,

I am currently building a custom genome where I am replacing 16 regions (50-300kb) with 16 regions of new sequence. What is the most efficient way of doing this? I have the coordinates of all regions in each chromosome where I want to paste the new sequence into and I have the files of the new sequences in .txt format.

Can you please advise?

Thanks