bacterial genome assembly with canu and alignment with reference genome with mauve

Question

[rthapa]

Hi, I have done de novo genome assembly of a bacterial strain with canu-2.1.1. The reference genome is available from the same bacterial strain. I compared the assembled genome with reference genome with mauve. I see the big chunk of genome part (1600Kb) present in different part of genome compared to reference genome. The reference genome and assembled genome are from the same bacterial strain. I wonder if this is due to any mistake in the genome assembly. I would appreciate any suggestion. Thanks

[GenoMax]

Have you looked at Mauve contig mover (LINK)? You may just need to rearrange things.

[rthapa]

I only have one contig. I wanted to see if it is aligned well. The assembled genome is from the same bacterial strain for which the reference genome is available. Could you please check the uploaded image in the following link? Thanks

https://ibb.co/58S4Cgr

[GenoMax]

That looks like just one major flip but the two pieces otherwise appear to be contiguous. Have you checked to see if the origin of replication is correctly identified in your assembly.