Merqury is a novel tool for reference-free evaluation of genome assemblies, utilizing efficient k-mer set operations. It estimates base-level accuracy and completeness by comparing k-mers in de novo assemblies to those in unassembled high-accuracy reads. For trios, Merqury can evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. The tool generates multiple visualizations, such as k-mer spectrum plots, to aid in evaluation. Merqury is demonstrated to be a fast and robust method for assembly validation on both human and plant genomes. Key features include consensus quality (QV) and k-mer completeness metrics, haplotype completeness, phase block statistics, and visual representations of phase consistency. Merqury's k-mer-based approach is more efficient and accurate than mapping-based methods, particularly for evaluating complex regions and heterozygous variants. The tool also provides efficient k-mer set manipulation capabilities through the Meryl k-mer counter. Overall, Merqury offers a comprehensive suite of methods for assessing assembly quality, completeness, and phasing, making it a valuable tool for genome assembly validation.Merqury is a novel tool for reference-free evaluation of genome assemblies, utilizing efficient k-mer set operations. It estimates base-level accuracy and completeness by comparing k-mers in de novo assemblies to those in unassembled high-accuracy reads. For trios, Merqury can evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. The tool generates multiple visualizations, such as k-mer spectrum plots, to aid in evaluation. Merqury is demonstrated to be a fast and robust method for assembly validation on both human and plant genomes. Key features include consensus quality (QV) and k-mer completeness metrics, haplotype completeness, phase block statistics, and visual representations of phase consistency. Merqury's k-mer-based approach is more efficient and accurate than mapping-based methods, particularly for evaluating complex regions and heterozygous variants. The tool also provides efficient k-mer set manipulation capabilities through the Meryl k-mer counter. Overall, Merqury offers a comprehensive suite of methods for assessing assembly quality, completeness, and phasing, making it a valuable tool for genome assembly validation.