I have 10 contigs presenting novel bacteria genome. How can I order them to fill gaps between with PCR?
Use progressiveMauve to order them relative to a reference.
Thanks. I don't have a reference. Should I use sequence of the closest related species?
Yeah that would probably be fine. Realistically you don’t necessarily need to re-order the contigs to close the gaps anyway. You can just design outward-looking primers to anneal to the end sequence you already have, and have it sequenced by Sanger sequencing.
Whatever you do, its probably going to be laborious though, since you don’t actually know how much missing sequence there is - those contigs are not going to connect directly to one another. I would suggest you look in to getting some Nanopore long read data to create a hybrid assembly.
The genome size is close to related species, so I think I will be able to fill the gaps with Sanger. Thanks for your suggestions and answer.
You may inspect the *.gfa or *.fastg files (with bandage). That may give you some hints about putative linkages between contigs.