You can have a look at the following on github. I used chromosomer with some success. I would first attempt an assembly vs C. elegans or another finished genome though. To be clear, with these programs you first need to do a de novo assembly, eg. with Abyss, soap-denovo etc

fenderglass / Ragout

Chromosome assembly using multiple references

gtamazian / chromosomer

A reference-assisted assembly tool for producing draft chromosome sequences.