I'm currently having issues trying to compare hybrid de novo assemblies of bacterial isolates to a reference genome (Using tools like Mauve, QUAST etc.). This because of the rotation/orientation of the contigs. I would like to know what the best (and easiest) way is to rotate my circular contigs from my polished Flye assembly to start at a dnA or repA protein (just like Unicycler does).
What my assembly looks like using Flye long-read assembly + Additional polishing
What my assembly looks like using Unicycler in hybrid mode.
Thanks in advance.