I have an assembled genome derived from PacBio long read data (assembled using canu). I would like to fish out both mitochondria and chloroplast contig sequence from the assembled data. Any software recommendation?
I tried to blast the assembled genome against NCBI blast but failed.
There is organelle genome in NCBI but I'm not sure how to make use of it as there is many link. Wondering how to make use of these information to achieve my objective https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/