Comparison Of Draft Genomes

Question

[nepgorkhey]

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.

Answer 1

[Josh Herr]

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.

See these answers for more information:

Help With Multiple Whole Genome Alignment. Aligning Over 400 Whole Genomes

Whole Genome Phylogeny

How To Do Multiple Whole Genomes Alignments?

Pairwise Genome Alignment

Phylogenetic Analysis Of Whole Genomes

[nepgorkhey]

Thanks a lot. I will definitely try your suggestions. The thing with MAUVE is that, as i was using draft genomes it showed lot of interconnections between the genomes. It was showing lot of rearrangements between the genomes that I was trying to look for but had lot of interconnecting lines showing the homologous regions. Thanks a lot for your suggestion. :)

[Josh Herr]

Your draft contigs are probably not ordered to your reference comparison so you will have to use the "re-order contigs" tool in Mauve to output your contigs to a different file -- you can then align them to your reference again or use another tool to close gaps in your alignment -- I like PAGIT, but there are others.