PDR

PDR computes a pairwise distance-based genome assembly evaluation metric that integrates completeness, contiguity, and correctness to enable holistic comparison of assemblies.

Key Features:

• Integrated quality dimensions: Combines completeness, contiguity, and correctness into a single evaluation metric for genome assemblies.
• Pairwise comparison: Enables direct, holistic pairwise comparisons between assemblies, reducing conflicts that arise when metrics are interpreted in isolation.
• Approximate fast implementation: Provides an approximate, faster implementation for large datasets with negligible approximation error demonstrated on public data.

Scientific Applications:

• Genome assembly evaluation: Quantifies overall assembly quality by integrating multiple assembly quality dimensions.
• Comparative assembly analysis: Ranks and compares multiple assemblies using a single pairwise distance metric to resolve conflicting metric signals.
• Scalable benchmarking: Applies to large assembly datasets using the approximate implementation validated on public data.

Methodology:

Integrates completeness, contiguity, and correctness into a pairwise distance reconstruction metric and provides an approximate, faster implementation for large datasets.