RT Journal Article
SR Electronic
T1 Efficient ancestry and mutation simulation with msprime 1.0
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.31.457499
DO 10.1101/2021.08.31.457499
A1 Franz Baumdicker
A1 Gertjan Bisschop
A1 Daniel Goldstein
A1 Graham Gower
A1 Aaron P. Ragsdale
A1 Georgia Tsambos
A1 Sha Zhu
A1 Bjarki Eldon
A1 Castedo E. Ellerman
A1 Jared G. Galloway
A1 Ariella L. Gladstein
A1 Gregor Gorjanc
A1 Bing Guo
A1 Ben Jeffery
A1 Warren W. Kretzschmar
A1 Konrad Lohse
A1 Michael Matschiner
A1 Dominic Nelson
A1 Nathaniel S. Pope
A1 Consuelo D. Quinto-Cortés
A1 Murillo F. Rodrigues
A1 Kumar Saunack
A1 Thibaut Sellinger
A1 Kevin Thornton
A1 Hugo van Kemenade
A1 Anthony W. Wohns
A1 H. Yan Wong
A1 Simon Gravel
A1 Andrew D. Kern
A1 Jere Koskela
A1 Peter L. Ralph
A1 Jerome Kelleher
YR 2021
UL http://biorxiv.org/content/early/2021/09/21/2021.08.31.457499.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.