At the outset, I would like to point out that I am an amateur in the field of NGS.
I've performed sequencing of prokaryotic genome (Alcaligenes faecalis with use of short (Illumina) and long reads (Nanopore). My goal is to fully resolve genome and mobilome structures with use of hybrid assembly (Unicycler).
Here comes the stupid question - how can I determine coverage depth? I should check FASTQ/FAST5 from both technologies separately?
thanks in advance,