NAToRA

NAToRA performs network-based relatedness pruning to remove related individuals from genetic and omics datasets while minimizing sample loss and preserving genetic diversity.

Key Features:

• Network-based relatedness-pruning: Constructs a relatedness network and prunes relationships to eliminate unwanted related individuals while minimizing dataset reduction.
• Node degree centrality metrics: Uses node degree centrality to identify highly connected nodes representing individuals in the relatedness network.
• Heuristic minimal-reduction algorithm: Employs heuristics that approximate minimal dataset reduction to retain the largest possible number of observations.
• Accepts multiple relationship metrics: Supports various relationship metrics as input for constructing the relatedness network.
• Comparative performance with PLINK and KING: Demonstrated superior relatedness-pruning versus PLINK and KING by removing all relatives while preserving a larger portion of the dataset and maintaining or enhancing genetic diversity.
• Genealogies simulator for testing: Includes a genealogies simulator used in testing and validation of the method.
• Scalability: Approach is suitable for large datasets where retaining maximal independent observations is critical.

Scientific Applications:

• Preparation of datasets for analyses requiring independence: Produces pruned datasets suitable for genetic and omics analyses that require independent observations.
• Preservation of genetic diversity: Enables downstream analyses to retain greater genetic diversity while removing related individuals.
• Method benchmarking and validation: Supports validation and benchmarking of relatedness-pruning approaches using the included genealogies simulator.

Methodology:

Constructs a relatedness network from pairwise relationship metrics, computes node degree centrality to identify highly connected individuals, and applies heuristics that approximate minimal dataset reduction to prune nodes and remove related individuals; a genealogies simulator was used for testing.