Improve a reference genome with sequencing data
One approach to this is to use whatever data you have to iteratively update the reference genome. You can keep chain files along the way so you can convert coordinates (e.g. in gff files) from the original reference to your new pseudoreference.

A simple approach might be:


Align new data to existing reference
Call variants (e.g. samtools mpileup, GATK, or whatever is best for you)
Create new reference incorporating variants from 2
Rinse and repeat (i.e. go to 1)


You can track some simple stats as you do this - e.g. the number of new variants should decrease, the number of reads mapped should increase, and the mismatch rate should decrease, with every iteration of the above loop. Once the pseudoreference stabilises, you know you can't do much more.