We are going to do 2 polishings to optimize our assembly: 1. Polishing with pilon using Illumina data 2. Polishing with racon and medaka using Nanopore data
If there is time we are also going to polish the racon/medaka polished assembly with Pilon and Illumina data.
A possible polishing with nanopolish is also included in this docs, but we are not going to use it in this course.