Figure 6.

Basic de novo genome assembly pipeline using long reads from ONT. This pipeline starts by filtering raw ONT long reads using FiltLong to discard short and low-quality reads. NanoPlot is then used to check the quality of both raw and filtered reads. The remaining reads are de novo assembled by using Flye. Resulting contigs from assembly are polished with multiple rounds of Racon and Pilon, in case that short reads of the same sample are available. Resulting assemblies can be assessed using QUAST and visualized with Bandage.