How to check for completeness of a mitochondrial or chloroplast genome?

Question

[kristina.mahan]

I used Novoplasty to get a circularized genome assembly for an algae chloroplast and algae mitochondria. How can I verify that these genomes are complete? Is there anything like BUSCO for organelle genomes?

[alex.zaccaron]

I am not aware of a dataset to estimate completeness of organelle genomes, but mitochondrial genomes should have a somewhat standard set of genes. Plus, they usually do not have a lot of genes, you could annotate your contigs and check the genes manually.

Answer 1

[kristina.mahan]

Looks like if I annotate with GeSeq I can verify that all the genes are present.