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.
This question is very common -- even just a few days ago someone asked this question: Any Software To Do Multiple Genome Alignment For Bacterial Genomes?
What kind of tool you are looking for? Mauve is really the standard with regard to what you are referring to. I am not sure what issues you are having with visualization, you don't understand the genome alignment output generated? I would argue that Mauve will not provide publication ready figures.
One of the key features of Mauve which I am not aware of in other synteny tools is the ability to re-order contigs. You can also use another synteny tool such as Symap or BRIG, but there are many tools out there. I would recommend Circos for visualization.
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