Author: Baumdicker, Franz; Bisschop, Gertjan; Goldstein, Daniel; Gower, Graham; Ragsdale, Aaron P.; Tsambos, Georgia; Zhu, Sha; Eldon, Bjarki; Ellerman, Castedo E.; Galloway, Jared G.; Gladstein, Ariella L.; Gorjanc, Gregor; Guo, Bing; Jeffery, Ben; Kretzschmar, Warren W.; Lohse, Konrad; Matschiner, Michael; Nelson, Dominic; Pope, Nathaniel S.; Quinto-Cortés, Consuelo D.; Rodrigues, Murillo F.; Saunack, Kumar; Sellinger, Thibaut; Thornton, Kevin; van Kemenade, Hugo; Wohns, Anthony W.; Wong, H. Yan; Gravel, Simon; Kern, Andrew D.; Koskela, Jere; Ralph, Peter L.; Kelleher, Jerome
Title: Efficient ancestry and mutation simulation with msprime 1.0 Cord-id: g62fwh9x Document date: 2021_9_21
ID: g62fwh9x
Snippet: Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements a
Document: Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and tskit library. We summarise msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
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