I've recently sequenced a bacterial genome using a combination of PacBio long read and Ilumina short read technology. What is peculiar about this particular bacterial species is that it harbors several plasmids of which one is quite small (3 kbp).
Now, I'm perfectly able to see many reads that map to the small plasmid reference (i.e., the coverage is high) from the Illumina short read sequencing data, while only a handful of long reads map to the same reference (i.e., those reads that originate from the PacBio seq. data).
What is your experience with the long reads and short DNA sequences? Is this the limitation of the PacBio technology or should I blame our sequencing center for filtering out the short fragments while processing the samples or the raw data?
It is a valid question to ask the sequencing center if they did something to exclude small fragments for PacBio sequencing. That could have happened as a part of the prep since with long read sequencing people want long reads so short fragments may be excluded.