I am trying to figure out the best way to fish for the organelle genomes from the assembled scaffolds. I know I can align/blast organelle genome from closely related species, but not sure if this is the best way to do it. Should I use the original
fastq files to do a reference based assembly (using closely related organelle genome)? Are there any program that can help me assemble just the organelle genome?
Any help will be greatly appreciated!
Thanks very much.