Scaffolding a genome with hybrid data
Try LR_Gapcloser.

I've used L_RNA_Scaffolder for trying to scaffold a genome (which turned out to be more complex than I had expected). It looks like LR_Gapcloser (written by the same people) is similar, but designed specifically for scaffolding using long-reads.

That page also suggests PBJelly and GMCloser as competing tools.