Aaron Darling and Andrew Tritt have written software to do parameter tuning who whole genome assembly using Mauve (which itself was written by Aaron Darling). A paper describing this software was published:
Darling AE, Tritt A, Eisen JA, Facciotti MT. 2011. Mauve Assembly Metrics. Bioinformatics. 2011 Oct 1;27(19):2756-7. Epub 2011 Aug 2.
Software is available here: http://ngopt.googlecode.com
Jonathan Eisen's Lab 