Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.

Genome Biol. 2019 Oct 28;20(1):224. doi:10.1186/s13059-019-1829-6

RaGOO: fast and accurate reference-guided scaffolding of draft genomes.

Aligns contigs to a reference genome with minimap2, and resolves structural variants with a modified version of Assemblytics that uses minimap2.