How to obtain organelle genome

Question

[wes]

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/

[lieven.sterck]

if full genome is not working out for you (though a correct approach) , you could select a subset of genes/proteins that are typically only present on those plastid genomes and use those for your blast.

looking at the GC content of the contigs/Scaffolds might also give you an indication

[wes]

Thanks. I have solved the issue by using "blat" program.

[kristina.mahan]

How did you use BLAT to pull out the organelle sequences?