Tools for comparative genomics through genome/pangenome maps

Question

[felipehcoutinho]

Hello,

I am currently working on a comparative genomic analysis of 24 bacterial genomes. I have been searching, without success, for tools that can produce genome maps that allow the visualization of similarities differences between these genomes. I am not interested in pairwise comparisons, but instead I need something that allows for the genomes of these organisms to be visualized simultaneously and compared to a reference genome, somewhat similar to figures 1 and 2 of this paper. Ideally that map should highlight differences in the structure of genomes (e.g. inversions and deletions). The best option I have found so far is the pangenome analysis from the GView Server, but it appears there is no downloadable version of the software, which requires the genomes to be uploaded to their servers and queued before processing. Any suggestions to carry out this task are appreciated. Thanks!

[Surati]

I'm working on similar project. Can you share if you found any better comparative visualization tool?

Answer 1

[thiagomafra]

Felipe, you know Circos? Figures 1 and 2 appear to have been created by him. I think he can help you.

• http://circos.ca/
• http://circos.ca/documentation/tutorials/
• http://circos.ca/documentation/course/

[felipehcoutinho]

Hi, thanks. I took a look at circos but as it turns out this tool is only for creating images, what I need is something actually does the genome comparissons and calculations that are used to create the genome/pangenome maps.

Answer 2

[zhush]

you can try CGView Comparison Tool, a very elegant and easily-used tool. CGView Comparison Tool