Running Mauve on circular genomes

Question

[Denis]

Hi! There are a batch of circular genomes i have to align with Mauve. The issue is that the genomes start at different positions. I'm wondering, if it's an important thing i should manage before the running of Mauve software ? I.e. should i somehow change the start coordinates in all the genomes so that these turn to be identical before the analysis?

Thanks!

[rthapa]

Were you able to solve the issue?

[Denis]

Hi! To get a nicer image representation it's important to set up the same start positions for all aligned genomes. I did it in a batch mode in Geneious software. Unfortunately i don't know any free software for that.

[rthapa]

I am working on bacterial genome. I assembled the genome with canu and polished with pilon. The genomes start at different positions. Do you have any idea if the structural variants detected by mauve will be correct in this case if I call variants without changing the arrangement of genome?

[Denis]

I think you will be able to figure out, which discrepancies are caused by the genome rearrangements and which ones just because of the different start positions by manual alignment inspection. E.g. i'd expect to see the same LCB at the somewhere in the beginning of some genome sequences, in the middle and even in the end for other ones just because of the differences in the residues numbering.

[rthapa]

Yes, I could figure it out after aligning with mauve (de novo genome assembly of bacterial genome) I am just concerned if calling structural variants without altering the genome would be fine.

[Denis]

I'm sorry, but i ran Mauve only for the whole genome alignments and comparisons, not for the variant calling. So, now i know nothing about how the algorithm actually works. You can open a separate post for that or try to get it from the software documentation.