We are planning to sequence a few bacterial isolates. We decided to go for PacBio and aim at getting a large insert library (20k) as the genome of the species is known for extensive presence of repeats. We hope to get in this way contiguous assemblies for the chromosome.
We worry about the plasmids. We know that some relatively short plasmids (6k - 15k) are likely to be present. If we go for large size selection (as described above) we are likely to lose these during the size selection step. It seems we might need a separate DNA extraction focusing on the plasmids (e.g. Qiagen Miniprep). And then we might need to submit these for sequencing separately. Obviously, for them a large library selection would be inappropriate. I wanted to ask: are there any recommended best practices when it comes to denovo assembly of plasmids, in particular shorter ones (less than 15k)?