Abstract Background Rapid and thorough quality assessment of sequenced genomes on an ultra-high-throughput scale is crucial for successful large-scale genomic studies. Comprehensive quality assessment typically requires full genome alignment, which costs a substantial amount of computational resources and turnaround time. Existing tools are either computationally expensive owing to full alignment or lacking essential quality metrics by skipping read alignment. Findings We developed a set of rapid and accurate methods to produce comprehensive quality metrics directly from a subset of raw sequence reads (from whole-genome or whole-exome sequencing) without full alignment. Our methods offer orders of magnitude faster turnaround time than existing full alignment–based methods while providing comprehensive and sophisticated quality metrics, including estimates of genetic ancestry and cross-sample contamination. Conclusions By rapidly and comprehensively performing the quality assessment, our tool will help investigators detect potential issues in ultra-high-throughput sequence reads in real time within a low computational cost at the early stages of the analyses, ensuring high-quality downstream results and preventing unexpected loss in time, money, and invaluable specimens.