Merqury

Merqury performs reference-free quality, completeness, and phasing assessment of genome assemblies using k‑mer analysis.

Key Features:

• Reference-Free Evaluation: Evaluates assemblies without reliance on a reference genome, enabling assessment of novel or highly divergent species.
• K-mer Based Analysis: Uses efficient k‑mer set operations to compare k‑mers from de novo assemblies with those in unassembled high‑accuracy reads (e.g., Illumina whole‑genome sequencing) to estimate base‑level accuracy and completeness.
• Haplotype-Specific Assessment: For trio datasets, evaluates haplotype-specific metrics including accuracy, completeness, phase block continuity, and switch errors.
• Visualization Outputs: Produces k‑mer spectrum plots and other visualizations to aid interpretation of assembly quality.
• Robustness and Speed: Applicable to genomes including human and plant species and reported to provide fast processing times and robust performance for large-scale projects.

Scientific Applications:

• De novo assembly validation: Provides reference-free estimates of base-level accuracy and completeness for validating de novo assemblies.
• Haplotype phasing evaluation: Assesses phasing quality in diploid organisms, including phase block continuity and switch error rates for trio datasets.
• Comparative and evolutionary genomics: Enables accurate assembly assessment for species lacking high-quality references to support comparative and evolutionary studies.
• Personalized medicine: Supports applications that require accurate individual genome assemblies for clinical or research use.
• Biodiversity and conservation genomics: Facilitates assembly assessment for non-model organisms in biodiversity and conservation studies.

Methodology:

Compares k‑mers between de novo assemblies and unassembled high‑accuracy reads (e.g., Illumina WGS) using efficient k‑mer set operations to estimate base‑level accuracy and completeness, evaluates haplotype-specific metrics for trio datasets including phase block continuity and switch errors, and generates k‑mer spectrum plots.