What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms

Question

[Matvii Mykhailichenko]

Hi guys!

I'm writing an article about de-novo assembling of eykariotic genomes of non-model organisms. I didn't find a guide for researchers how to sequence such sample. Do we have to first separate nuclear from mito genomes to make assemblies better? And then process them separately.

I would be grateful for any link or comment. Have a great day!