Let's say I have two fragments of bacterial DNA (~50kb in length each) that overlap on the ends by roughly ~10kb; the overlap sequences are unknown. I would like to assemble these into longer fragments (in vitro) in some way, but the methods I've found so far rely on 24-40bp known overlaps (e.g., the isothermal assembly process in DG Gibson et al., Nature Communications 2009).
Anyone have any idea? I'm kind of new to this molecular biology stuff, so if this is an open problem, I apologize. I'm mainly just making sure I'm not overlooking something obvious. For all I know, there could be a standard protocol for this. Thanks in advance!