I am working first time on de novo assembly. I am working on mitochondrial genome assembly of plant species. My expected genome size is about ~800KB and after velvet+AMOS use it is coming around ~1.1MB. I am further extending my analysis for gene prediction where I am currently stuck. I sought for your advices and help for gene prediction and annotation for Plant Mitochondrial genome. So far, I have used Mitofy but not sure of its result. Is RepeatModeler fine for plant mitochondrial genome?
I think you should frame your question to include word "plant mitochondria", so that people can search your post using those key words.
Good suggestion. Done !