Bacterial Synteny Tools

Question

[John]

Hi,

I'm trying to generate some synteny plots for >10 whole bacterial genomes can anyone suggest some tools? These genomes are ~2.3 mb and contain a lot of rearrangment and repeats.

Cheers

Answer 1

[sansan_96]

Hello,

I have used TBtools to make multiple syntenys (https://github.com/CJ-Chen/TBtools-II) and for more attractive visualization I have used SynVisio (https://synvisio.github.io/#/)

Answer 2

[cmdcolin]

some possible tools

progressiveMauve gggenomes gggenes genoplotR pyGenomeViz clinker plotsr

from looking at https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Comparative

Answer 3

[Joe]

clinker and sibeliaX are the best IMO.

Sibelia in particular is designed for exactly this task and can even produce plots of all vs all comparisons, which most other tools won't.