I have assembled a draft genome of s. pombe that I would like to compare to the reference. My purpose is to study structural variations (rearrangements, insertions/deletions, etc.) between the two genomes. Mauve is a good tool that has been serving my purpose thus far, but it turns out that it doesn't detect duplications, i.e. if a sequence from the reference is found twice in the draft genome; it only aligns it to one of them, and the other is labelled as not mapped.
The features that I'm looking for in in an aligner are the following:
1. Detecting duplications and labelling them.
2. Good detailed output, including for example non-mapped contigs, contigs with multiple alignments, contigs with break-points (contigs that have a part mapped to one region and another part mapped to a different region.)
3. Quality, publication-fit figures.
4. Moves contigs to where they mapped in the reference (like Mauve contig mover).
I hope that there exits a software that does all of that.