I want to detect NUMTS (nuclear mitochondrial sequences) that have migrated from the mitochondrial to the nuclear genome using the whole genome sequence data. What could be the best Bioinformatic approach? Their presence, extent and frequency of migration of mitoDNA into nuclear DNA is unknown.
Currently, I am trying to align the raw sequenced data with the nuclear reference genome followed by the command line BLAST where I use the mitochondrial genome as Query against the database of nuclear reference genome of the same species.
Is that the correct approach?
For context, about 90% of the mitochondrial genome is susceptible to insertion into the nuclear genome. These insertion events occur throughout an individual's lifespan with regular frequency (usually in DSB repair), and have been occurring for basically the entirety of organism evolution.
Thank you in advance for all your helpful suggestions and comments.