Hi everyone!

I'm quite new to this genomics stuff, so sorry if this question seems silly (or just cheeky). I have looked for similar questions, but haven't found any (but I'm terrible at searching, though).

So. I have Illumina reads for a E.coli strain that has GFP inserted in it. I know roughly where the GFP should be, and I have the reference genome for the unmodified E.coli strain. I want to assemble a new reference for my modified strain.

From what I've seen so far, the idea would be to do a de novo assembly, then some scaffolding and mapping to the reference I have, using something like Mauve. But as my sequences map almost perfectly to the reference, and the only important breakpoint is the GFP insertion, can't I use this information to improve my assembly? If so, how? 

Thanks!
Pablo
It's called reference guided assembly. Many assemblers can do it..