Forum:What's the state of the art in bacterial whole genome alignment?

Question

[Dave Carlson]

Hi All,

I need to align ~ 8 whole bacterial genome assemblies and visualize the shared and unique regions in each genome. My initial plan is to use progressiveMauve + PyGenomeViz for this task. However, I noticed that mauve has not been updated since 2015, so I'm curious if there is a better tool that the community has adopted in place of mauve?

Thanks! Dave

[GenoMax]

Are these related genomes and do you really need to align them at the genome level?

If a tool is mature (and still works) then it should not matter if it has not been updated.

[Dave Carlson]

They are all strains of the same species. The investigator has reasons to believe that some samples will possess genomic regions not present in all samples and wants to find these, so yes, I think whole genome alignment may be the easiest way to confirm that.

As my question indicated, I was mostly curious if the community is still using mauve/progressiveMauve for bacterial genome alignment or if other tools have supplanted it.