ancestryinfer

ancestryinfer performs local ancestry inference and coupled demographic and sequencing simulations to quantify genomic contributions from parental species within hybrid genomes.

Key Features:

• Simulation (mixnmatch): Uses mixnmatch to simulate complex demographic histories of parental and hybrid populations, including selection on hybrids and technical variables such as sequencing coverage and contamination, and supports arbitrarily complex demographic scenarios.
• Local ancestry inference (ancestryinfer): Processes sequencing reads from simulated or real individuals through an analysis pipeline to infer local ancestry and identify genomic regions derived from different parental species.
• Paired simulation–analysis pipeline: Couples mixnmatch simulations with ancestryinfer analyses to evaluate and predict local ancestry inference performance under varying biological and technical parameters.
• Performance assessment: Identifies critical parameters that influence the accuracy of local ancestry inference via simulation experiments.

Scientific Applications:

• Hybrid genome analysis: Dissects genomic architecture shaped by hybridization by mapping parental-origin regions within hybrid genomes.
• Method benchmarking and study design: Enables benchmarking of local ancestry inference methods and planning of experiments by simulating sequencing coverage, contamination, and demographic scenarios.
• Cross-disciplinary research: Applies to human genetics, ecology, and evolutionary biology for studying admixture, hybridization, and their genomic consequences.

Methodology:

Performs simulations with mixnmatch to generate demographic and technical scenarios and processes sequencing reads through the ancestryinfer analysis pipeline, using paired simulation and analysis workflows to assess local ancestry inference performance.