DandD

DandD quantifies sequence novelty and similarity in expanding genome assembly collections using the delta (δ) measure and genomic sketches to assess sequence growth and redundancy.

Key Features:

• Delta-based quantification: Uses the delta (δ) measure, originally developed for data compression, to quantify novel sequence and redundancy based on k-mer counts.
• Genomic sketches: Employs genomic sketches (compact genome representations) to rapidly estimate delta values and reduce dependence on explicit k selection.
• K-independent Jaccard calculation: Substitutes delta for k-mer-specific cardinalities when computing the Jaccard coefficient to produce k-independent all-pairs similarity estimates.
• Structural variation reporting: Describes structural variations discovered in each new human genome assembly and assesses when discovery rates may plateau.
• Pangenome growth metrics: Quantifies how much novel sequence is gained as a collection expands and characterizes pangenome expansion rates.

Scientific Applications:

• Sequence growth assessment: Measure sequence novelty and redundancy across rapidly expanding genome assembly databases.
• Pangenome dynamics: Characterize pangenome expansion rates and estimate saturation or plateau of novel discovery.
• Genome similarity comparisons: Compute k-independent all-pairs similarities among assemblies using delta-based Jaccard approximations.
• Structural variation surveillance: Track discovery of structural variants across successive human genome assemblies and evaluate discovery trends.

Methodology:

Computations use the delta (δ) measure derived from data compression and k-mer counts, estimate δ via genomic sketches, and replace k-mer-specific cardinalities with δ when computing the Jaccard coefficient for k-independent all-pairs similarity.