LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, another draft genomes, etc)
Paper at https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0076-3
