I'm working on a bunch of small viral genomes, and I need to construct their core genomes for a comparative study. I've tried using prokka and roary to do so, but since my sequences are too small ( 10 kb or less). I keep getting errors and warnings even though I obtain an output, and I keep getting 0 core genes from roary. It turned out that prokka uses a tool called Prodigal, and the sequence size threshold it uses is 20kb. So eventually, I can't get GFF3 files from prokka to run roary. Now I'm left with one of two solutions:
1/ look for an other source of GFF3 files to run roary and get my core genomes. 2/ Try something else (other than roary) to generate core genomes.
If you happen to know other tools or scripts I can use in my case please let me know. Many thanks!!