I have some fungal genomes that I downloaded from NCBI, it appears that 5 of the genomes have not been annotated. I have a set of Blast hits, and I want to see if I can match the locations of the hits to see if they overlap with any gene models. Initially, I tried uploading the genomes to fgenesh, as I have no experience annotating genomes. However, fgenesh just produced an error message (I think the files were too big).
I have since tried to use maker, but I'm having trouble with it. Are there any alternatives to fgenesh online that can handle larger files (~ 49MB)? Is there a way of using maker that produces annotations to a similar standard without it taking days? I understand that maker can be run and trained using SNAP, AUGUSTUS etc, but I'm not sure that is necessary and I think it will end up taking me forever, as I don't really understand the process.
Any advice would be much appreciated