How to extract mitgenomes from WGS data for non model organisms ?

Question

[sunnykevin97]

HI

Suppose if we have ~30-40 X coverage genome data, how to extract mitogenome from whole genome data. I saw some pipelines (Norgal & MitoZ) do that. It doesn't work well for my data. Hardly recovered ~10kb single or multiple contigs representing only half of the mitogenome.

Any suggestions.