Tumour cells exhibit frequent copy number aberrations and as a consequence widely vary in their ploidy. Accurately estimating cell ploidy from sequence data alone is challenging. scAbsolute is the first tool to identify different ploidy states based only on read density. We demonstrate that scAbsolute achieves accurate and unbiased mea- surement of single-cell ploidy and replication status, including whole-genome duplications. It provides a robust foundation for single-cell DNA sequencing analysis across different technologies and enables improvements in a number of downstream anal- ysis, such as copy number calling, quantification of intratumour heterogeneity, and reconstruction of tumour evolutionary phylogenies.

These are the results obtained when running the respective tools. They make it possible to reproduce the figures and the analysis in the manuscript without re-running all scripts. In addition, we provide the raw read counts that have been used to create the bin annotations for the scAbsolute software.