Measuring satellite arrays of the human Y chromosome from sequencing reads

Human Y chromosome satellites vary widely but remain difficult to measure in large cohorts. In response, we developed Yruler, which uses pangenome assemblies to measure satellite lengths, composition and Y dosage from sequencing reads without alignment. Analyses reveal centromere-length differences between related lineages, extend observations of short non-centromeric arrays across a lineage, and show unequal component variability and composition changes with heterochromatin length within lineages. Yruler brings satellite variation into population-scale phenotype studies.