There are many ways to do this. I suggest to do the following:
1) Align your genome to the reference genome using pairwise megablast
2) From the alignment you'll be able to find the position of your genome that corresponds to the first position in the reference. Then change your genome sequence, so now it starts from this position.
3) Align your genome to the reference genome again and look at the dotplot. You'll be able to see structural differences on the dotplot.

I think Quast is a good tool for that. It already aligns the assembly to the reference independently of any issue with circularity. I think it's also useful to get two different assemblies with two different software. Sometimes it's just the assembler that fails.

Here you have a likely real rearrangement verified by three different algorithms (SPAdes, rnaSPAdes and Contignant s-aligner):

Here you have a false rearrangement detected with SPAdes