What bioinformatics tool can be used to get good comparison of draft genomes from bacteria. The size of genome is approximately 5 mb and I have tried to use MAUVE and Mummer which have resulted outputs that are hard to read and a lot messy with number of contigs. I have about 80 contigs for the draft genomes that i am working and want to have a good way of visualizing the differences with the reference genome. I have used DNA diff to find the percentage difference already. What could be further suggestions.