My dear nerd community,
We are sequencing many genomes of non-model plants today.
One of the first task is to separate the plastid, the mitochondrial and the nuclear genome. I was thinking there was general guidelines or even a consensus way to do it, but not really
I have to specify, in this case we do not have any close related reference genomes (nuclear or plastid or mitochondrial), we like challenges!
So what we do in our lab:
1. Download from NCBI one file for all plastid and the all mitochondrial genomes
2. Use mirabait tool from MIRA package to separate the different genome
3. Do your assembly for your plastid genome or nuclear genome
Do you have a better way to do it? Because this method is not that perfect.