Merfin

Merfin applies k-mer multiplicity analysis to filter variant calls and polish genome assemblies, improving genotyping accuracy for long-read sequencing data (PacBio HiFi, PacBio CLR, Nanopore).

Key Features:

• K-mer-based filtering: Uses k-mer multiplicity from sequencing reads to evaluate and filter variant calls independently of read alignment quality and internal variant-caller scores.
• Improved precision and error reduction: Enhances variant call precision and reduces frameshift errors in long-read assemblies generated by PacBio HiFi, PacBio CLR, or Nanopore.
• Assembly-quality metrics: Computes novel metrics of assembly quality and completeness that incorporate expected genomic copy numbers.

Scientific Applications:

• Genome polishing: Polishes high-quality genomes to improve base-level accuracy and variant sets.
• Human genome refinement: Applied to refine the first complete human genome and fully phased human genomes.
• Non-human assemblies: Improves accuracy and reduces errors in non-human high-quality assemblies.
• Downstream genotyping analyses: Produces more reliable variant calls for downstream genomic analyses.

Methodology:

Analyzes k-mer multiplicities in sequencing reads to assess the likelihood of variant calls, computes expected k-mer multiplicities and copy-number-aware assembly metrics, and avoids reliance on alignment quality or variant-caller scores.