Finally I went trough contamination in bacteria genome (circular) , and now I would like to reorder contigs (less than 20). I used mauve contig mover for this purpose (http://darlinglab.org/mauve/user-guide/reordering.html). I am not sure if it is a good solution cause my bacteria is novel and it's hard to define the closest species. Anyway I have ordered contigs where 7 of them are "Contigs with conflicting ordering information". This means that I cannot say whether those 7 contigs are welled ordered.
I was trying to map contigs into possible closest one species and then see what is the ordering, but it ended up with a lot of multiple aligments and breaks.
I would like to annotate contigs with prokka, but to do that I need to know the ordering of contigs to not miss any genome element.
How can I order contigs to make results reliable annotated?
Many thanks, Agata