How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?
You might want to look into Unicycler (manuscript with more information can be found here); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome such as a mitochondrion's.



Beware that if you happen to have very long reads, you might end up with an assembly with multiple copies of the circular genome: you might want to look into circlator then.