I am looking for a tool to do assembly to assembly mapping for bacteria and I am very excited to have found minimap2!

Do you have a best practices document for this use case?

Or is minimap2 -ax asm5 ref.fasta query.fasta > alignment.sam the way to go?

Edited to add that I am specifically curious about how to annotate differences between the two assemblies (i.e. SNPs, indels, etc).

Thanks!
~Lina