I want to compare two bacterial genomes that will be sequenced with nanopore. Can someone assist with the galaxy programs that I can use to see if there are difference in the genomes. The idea is to see if they mutate through passaging in order to create a vaccinal strain. I also want to compare with the wild type strain. I saw that Chromeister can be used but I need help interpreting the results.
Thanks
Welcome, @PhD_Nikolay_Anachkov
These two tutorials use SNPs for genomic evolution analysis
Others are welcome to comment/suggest more! 
Dear Jennaj,
thank you for this feedback. I will check this out. It will be helpful for sure!!!