Question: Order of contigs
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Joe ♦ 18k wrote:
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?
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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.
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