Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA-a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10xe2x80x89xc3x97xe2x80x89Genomics.