I'm currently working on a de novo genome assembly on a novel bacterium using nanopore and illumina data. I have done multiple assemblies and found that my best results came from Canu and MaSuRCA but I am now unsure of how to proceed. I believe I need to polish my assemblies and I have looked into nanopolish, medaka, and pilon but I am uncertain how to measure the success of polishing and subsequently which assembly/polish method I should proceed with afterwards. What metrics can I use for comparisons without the need for a reference genome to help accomplish this?
Thank you in advance!