FASTQuick: Rapid and comprehensive quality assessment of raw sequence reads

Background Rapid and thorough quality assessment of sequenced genomes in an ultra-high-throughput scale is crucial for successful large-scale genomic studies. Comprehensive quality assessment typically requires full genome alignment, which costs a significant amount of computational resources and turnaround time. Existing tools are either computational expensive due 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 raw sequence reads without full genome 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 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, ensuring high-quality downstream analysis and preventing unexpected loss in time, money, and invaluable specimens.