Hi,

Which aligner do you recommend to use for OmicCircos or Rcircos in order to create synteny plots between a reference genome (contains chromosomes and annotation) and a contig based assembly without annotation? 

Which alignment format should be produced and are there any code examples which show how to extract the required information from the alignment file and put them in the correct format OmicCircos or Rcircos?

Thank you in advance.