optical map & assembly

Question

[bobo]

If you have an optical map of a bacterial genome and wanted to do an assembly (with unpaired reads) guided by an optical map how would you go about doing it.

Does any one know of a software that is already made that may be able to do this? Any recommendations would be appreciated

Thanks

Answer 1

[rtliu]

You could try SOMA (Scaffolding using Optical Restriction Mapping):

Command line version: http://www.cbcb.umd.edu/software/soma

Web-based version: http://www.cbcb.umd.edu/soma/index.php

Published paper: http://bioinformatics.oxfordjournals.org/content/24/10/1229.short