Method for comparing denovo to reference assembly

[splaisan]

I obtained a non-sorted assembly (contigs) which I would like to:
* compare to the expected reference genome (available as fasta, gff, gbk)
* sort and re-orientate the contigs to best match the reference
* plot xy diagonal between the sorted and the ref
* generate AGP file describing the matches and gaps between the two

Can someone please propose best tools and ideally tutorial pages to do this.

So far I used nucmer+mummer-plot and mauve but they do not provide the AGP and plots are not so nice. I am confident there is better out there.

Thanks
Stephane