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Thanks for your work on this software. I like using the standalone unicyclcer_polish
module to polish assemblies generated using long-read assemblers. I noticed in the unicycler documentation that the full unicycler pipeline will rotate circular contigs between rounds of polishing (if I'm reading it correctly). Watching the unicycler_polish log, it doesn't appear that circular contigs are rotated in the standalone module. Is there a way to get the standalone module to recognize contigs as circular and rotate them as in the full pipeline? Alternatively, it would be great to be able to set a flag to rotate all/some contigs between polishing rounds.
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