The short length of reads from current high-throughput sequencing technologies leads to ambiguities when mapping the genomic location of these reads. Kaplan and Dekker show that Hi-C chromosome conformation capture data, which report the three-dimensional (3D) proximity of DNA regions in cells, contain valuable information on the cis-connectivity of DNA. Supplementing human sequence contigs with Hi-C data from human cells facilitated the mapping of previously unmapped contigs and the de novo assembly of a genome scaffold. The method may be applicable to genomes of various species.