I have 12 scaffolds that need to be connected with Sanger PCR products. I would like to design starters for all sequences. Is there a tool that can do that automatically?
I've tried CONTIGuator - it didn't help, cause my novel bacteria and it's related species reference sequence just don't match. The output is "No contigs mapped to reference! Exiting..."
So, is there a tool that can automatically design starters and fill gaps between scaffolds without genome reference?
Many thanks for any suggestions.