Abstract Summary Single-cell DNA template strand sequencing (Strand-seq) enables chromosome length haplotype phasing, construction of phased assemblies, mapping sister-chromatid exchange events and structural variant discovery. The initial quality control of potentially thousands of single-cell libraries is still done manually by domain experts. ASHLEYS automates this tedious task, delivers near-expert performance and labels even large datasets in seconds. Availability and implementation github.com/friendsofstrandseq/ashleys-qc, MIT license. Supplementary information Supplementary data are available at Bioinformatics online.