Meryl

Meryl counts and manipulates k-mer sets to enable efficient k-mer set operations for k-mer–based genome assembly analysis and reference-free assembly validation.

Key Features:

• K-mer counting: Counts k-mers (subsequences of length k) derived from DNA sequences.
• K-mer set operations: Performs efficient k-mer set operations for comparing and manipulating k-mer collections.
• Integration: Originated in the Celera Assembler and has been integrated into Canu.
• Merqury support: Provides k-mer operations used by Merqury to compare assembly k-mers to those in high-accuracy unassembled reads.
• Trio and haplotype analyses: Enables assessment of haplotype-specific metrics including accuracy, completeness, phase block continuity, and switch errors in trios.
• K-mer spectrum outputs: Produces k-mer spectrum plots for inspection of assembly characteristics.
• Performance: Demonstrated robustness and speed across organisms including human and plant genomes.

Scientific Applications:

• De novo assembly evaluation: Evaluates de novo genome assemblies by comparing k-mer content without relying on a reference genome.
• Base-level accuracy and completeness estimation: Estimates base-level accuracy and assembly completeness by comparing assembly k-mers against high-accuracy unassembled reads (via Merqury).
• Haplotype evaluation in trios: Assesses haplotype-specific accuracy, completeness, phase block continuity, and switch errors in trio assemblies.
• Long-read assembly validation: Applicable to validating long-read assemblies that may exceed existing reference genome quality.
• Cross-species validation: Applied to genomes including human and plant for robustness and speed demonstrations.

Methodology:

Counts and manipulates k-mers and performs efficient k-mer set operations, compares k-mers between de novo assemblies and high-accuracy unassembled reads (used by Merqury), supports trio-based haplotype-specific comparisons, and outputs k-mer spectrum plots.