Hi Noopur Joshi for bacteria genomics this is what I usually do.Maybe you can adapt to your data.

I perform de novo assembly(software depends on the platform).If its nanopore you can use flye or canu. I then perform reference guided scaffolding using RagTag( i.e. If your organism has a reference genome available) to generate scaffold. RagTag using minimap to do map the reads to the reference genome. The final sequence you get will be the reads that mapped to the reference genome. You can do a genome comparison of your genomes using BRIG. I made a tutorial for that here (https://youtu.be/pobQgE4z-5Q)

Thanks for the help. Vincent Appiah

Interested