post de novo assembly reference mapping?

[smoics]

I am curious if there is a program/app that would do post de novo assembly reference mapping--essentially breaking down the full scaffold into chunks and reference mapping it post-assembly.

I do recognize that I could alternatively use a software to reference map while doing the initial assembly. Just exploring options.

[SNPsaurus]

The bbtools program shred.sh will break a reference into chunks which can then be used for alignment. I'm not totally sure that is what you are looking for but it is my best bet!