BLAST Ring Image Generator (BRIG) is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at: http://sourceforge.net/projects/brig

BRIG can generate figures like this in a matter of minutes:

BRIG_example
From Totsika et al. (2011) ‘Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms.’, PLoS ONE 6(10): e26578.
doi:10.1371/journal.pone.0026578

Please cite the BRIG paper if BRIG is used to generate figures for publications:

NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011). BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423 https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402