Here are a couple of tools for SV detection you may want to look into that I've been reading about lately (just today!), but haven't tried:

• Variation Hunter
• Hydra

Any feedback on how these systems perform would be helpful for the community.

I myself have not tried using any of these tools, but this type of analysis is in my TODO list. I found this a couple of days ago and it looks very promising:

http://bioinf.spbau.ru/en/sibelia

From their website:

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

In version 2, Sibelia works with multiple strains of bacteria and partitions their genomes into synteny blocks — blocks of highly conserved regions among all compared genomes. It represents genomes in circos pictures [for publication] or interactive forms [for experts’ analysis].

Sibelia is under active development. If you see that Sibelia has a potential to support your research, please do not hesitate to contact us at vyahhi@bioinf.spbau.ru with a list of features you would like Sibelia to have.

You might have a look at breakway ("Identify Structural Variations in Genomic Data").

Even Sibelia has a web interface:

https://etool.me/software/sibelia

https://etool.me/software/csibelia

can we use C-Sibelia OR sibelia for more than two genome, if so what would be the command line