Putnam et al. report an in vitro method for generating long-range linkage data that improves the scaffolding of de novo assembled genomes. Their approach, called Chicago, requires only small amounts of high-molecular-weight DNA as starting material and uses reconstituted chromatin as a substrate to produce proximity ligation libraries. Using the HighRise (HiRiSE) software, genomic scaffolds can be generated. The authors show the utility of their method for human genome assembly and scaffolding. Moreover, Chicago libraries can be used to improve existing assemblies, which the authors illustrate by reassembling and scaffolding the genome of the American alligator, and for haplotype phasing.