Smudgeplots

Smudgeplots analyzes heterozygous k-mer pairs from whole-genome sequencing reads to profile polyploid genome structure and infer ploidy without a reference genome.

Key Features:

• Haplotype structure visualization: Generates visual representations of haplotype structures by examining heterozygous k-mer pairs from raw or trimmed reads.
• Reference-free profiling: Profiles genome composition and ploidy directly from sequencing reads without requiring a reference genome.
• Heterozygous k-mer extraction: Extracts heterozygous k-mer pairs from k-mer dump files for downstream analysis.
• Coverage-based inference: Uses the sum of k-mer pair coverages (CovA + CovB) and the coverage ratio CovA / (CovA + CovB) to disentangle genome structure and infer copy number relationships.
• K-mer frequency-based genome estimates: Estimates genome characteristics such as size, heterozygosity, and repetitiveness through k-mer frequency analysis.
• Application to complex and variable ploidy genomes: Applied to systems with variable ploidy including Meloidogyne species and octoploid Fragaria x ananassa.

Scientific Applications:

• Genome profiling prior to assembly: Provides estimates of genome size, heterozygosity, and repetitiveness to inform assembly strategies.
• Polyploid genomics: Enables analysis of ploidy levels and heterozygosity structure in polyploid organisms, including plants.
• Analysis of variable-ploidy systems: Supports investigation of genomes with duplications or varying ploidy, as demonstrated in Meloidogyne and Fragaria x ananassa.

Methodology:

Extract heterozygous k-mer pairs from k-mer dump files and analyze their coverages using the sum (CovA + CovB) and ratio (CovA / (CovA + CovB)), leveraging combinatorial theory as described in the GenomeScope 2.0 framework.