Hi, I have been trying to assemble E. coli genome and I have both Illumina and Nanopore reads. I used unicycler to assemble my genome and assess the quality of the assembled genome using Quast against the reference E. coli genome. I got about 5 misassemblies according to Quast and I am not sure how to fix this misassemblies. I tried the assembly again in Unicycler with a ‘conserved’ mode but the misassemblies are still there.
How do I fix this? any help is appreciated!