A lab that works with ours does pretty frequent MiniSeq runs. I was going to sequence this 12 kb plasmid (which we have almost no information about) by Sanger sequencing, then ordering new primers based on those sequencing, then sequencing further down the plasmid, etc. until the whole thing is sequenced; but this could take weeks.
Could I just fragment the plasmid (e.g. by sonication), ligate on Illumina adapters, index by PCR, and include it with the next MiniSeq?
Sure, why not. But then need to have a workflow for data processing and assembling.
But don't you think a MiniSeq run for just 1 plasmid will be overkill and expensive?
Most plasmids contain at least one standard sequence of something like M13 that flanks the insert/multi-cloning site. Test if those primers will amplify a product. If yes, send in the plasmid for sequencing starting from those sites. You'll have to design new primers from the sequence data & do a "walk" around the plasmid to get the full sequence.
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