Clarity for -c option

[Xevkin]

Hi. Could I ask for clarity on the -c option for mia. The help information for the parameter says "means reference/assembly is circular". Does this mean that A) the reference has been circularized, there is duplicate sequences at the beginning and end of the reference, or B) the reference comes from a circularized sequence e.g. it is a linear representative of a circularize molecule. Thanks.

[aersoares81]

It means it comes from a circularised sequence. So you don't have to add duplicate sequences at the beginning and end.