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Modern genomics depends on inexpensive short-read sequencing. Sequenced reads up to a few hundred base pairs in length are computationally mapped to estimated source locations in a reference genome. These read mappings are used in myriad sequencing-based assays. For example, through a process called genotyping, mapped reads from a DNA sample can be used to infer the combination of alleles present at each site in the reference genome.

A single reference genome cannot capture the diversity within even a single person (who gets a genome copy from each parent), let alone in the whole human population. Genomes differ not only by point variations, where one or a few bases are different, but also by structural variations, where differences can be much larger than an individual read. When a person’s genome differs from the reference by a structural variation, the …