I'm trying to optimize TraDIS for our model bacterium and I am having some technical problems with the DNA preparation for the sequencing step.

I'm struggling with efficient PCR enrichment of mariner transposon/chromosome junctions which is critical to the success of TraDIS experiments (as only one mariner transposon insertion is expected to occur per genome).

I'm using NEBNext® Ultra™ II DNA Library Prep Kit and noticed the presence of large fragments (>1500 bp) in our final libraries. The solution might be the use of “splinkerette” adapters instead of the generic adaptors provided by the NEBNext kit and I was wondering if someone here has experience with designing it (and subsequent primers) for mariner transposon, and might advise me on how to do it? I would really appreciate any help like optimized protocol/piece of advice/tips!