Efficient ancestry and mutation simulation with msprime 1.0

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Efficient ancestry and mutation simulation with msprime 1.0. / Baumdicker, Franz; Bisschop, Gertjan; Goldstein, Daniel; Gower, Graham; Ragsdale, Aaron P.; Tsambos, Georgia; Zhu, Sha; Eldon, Bjarki; Ellerman, E. Castedo; Galloway, Jared G.; Gladstein, Ariella L.; Gorjanc, Gregor; Guo, Bing; Jeffery, Ben; Kretzschumar, Warren W.; Lohse, Konrad; Matschiner, Michael; Nelson, Dominic; Pope, Nathaniel S.; Quinto-Cortes, Consuelo D.; Rodrigues, Murillo F.; Saunack, Kumar; Sellinger, Thibaut; Thornton, Kevin; Van Kemenade, Hugo; Wohns, Anthony W.; Wong, Yan; Gravel, Simon; Kern, Andrew D.; Koskela, Jere; Ralph, Peter L.; Kelleher, Jerome.

In: Genetics, Vol. 220, No. 3, iyab229, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Baumdicker, F, Bisschop, G, Goldstein, D, Gower, G, Ragsdale, AP, Tsambos, G, Zhu, S, Eldon, B, Ellerman, EC, Galloway, JG, Gladstein, AL, Gorjanc, G, Guo, B, Jeffery, B, Kretzschumar, WW, Lohse, K, Matschiner, M, Nelson, D, Pope, NS, Quinto-Cortes, CD, Rodrigues, MF, Saunack, K, Sellinger, T, Thornton, K, Van Kemenade, H, Wohns, AW, Wong, Y, Gravel, S, Kern, AD, Koskela, J, Ralph, PL & Kelleher, J 2022, 'Efficient ancestry and mutation simulation with msprime 1.0', Genetics, vol. 220, no. 3, iyab229. https://doi.org/10.1093/genetics/iyab229

APA

Baumdicker, F., Bisschop, G., Goldstein, D., Gower, G., Ragsdale, A. P., Tsambos, G., Zhu, S., Eldon, B., Ellerman, E. C., Galloway, J. G., Gladstein, A. L., Gorjanc, G., Guo, B., Jeffery, B., Kretzschumar, W. W., Lohse, K., Matschiner, M., Nelson, D., Pope, N. S., ... Kelleher, J. (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220(3), [iyab229]. https://doi.org/10.1093/genetics/iyab229

Vancouver

Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G et al. Efficient ancestry and mutation simulation with msprime 1.0. Genetics. 2022;220(3). iyab229. https://doi.org/10.1093/genetics/iyab229

Author

Baumdicker, Franz ; Bisschop, Gertjan ; Goldstein, Daniel ; Gower, Graham ; Ragsdale, Aaron P. ; Tsambos, Georgia ; Zhu, Sha ; Eldon, Bjarki ; Ellerman, E. Castedo ; Galloway, Jared G. ; Gladstein, Ariella L. ; Gorjanc, Gregor ; Guo, Bing ; Jeffery, Ben ; Kretzschumar, Warren W. ; Lohse, Konrad ; Matschiner, Michael ; Nelson, Dominic ; Pope, Nathaniel S. ; Quinto-Cortes, Consuelo D. ; Rodrigues, Murillo F. ; Saunack, Kumar ; Sellinger, Thibaut ; Thornton, Kevin ; Van Kemenade, Hugo ; Wohns, Anthony W. ; Wong, Yan ; Gravel, Simon ; Kern, Andrew D. ; Koskela, Jere ; Ralph, Peter L. ; Kelleher, Jerome. / Efficient ancestry and mutation simulation with msprime 1.0. In: Genetics. 2022 ; Vol. 220, No. 3.

Bibtex

@article{7064bbd6aa544fdb8c3a8d853f4b30b8,

title = "Efficient ancestry and mutation simulation with msprime 1.0",

abstract = "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, a large number of specialized 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 the tskit library. We summarize msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized 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. ",

keywords = "Ancestral Recombination Graphs, coalescent, mutations, Simulation",

author = "Franz Baumdicker and Gertjan Bisschop and Daniel Goldstein and Graham Gower and Ragsdale, {Aaron P.} and Georgia Tsambos and Sha Zhu and Bjarki Eldon and Ellerman, {E. Castedo} and Galloway, {Jared G.} and Gladstein, {Ariella L.} and Gregor Gorjanc and Bing Guo and Ben Jeffery and Kretzschumar, {Warren W.} and Konrad Lohse and Michael Matschiner and Dominic Nelson and Pope, {Nathaniel S.} and Quinto-Cortes, {Consuelo D.} and Rodrigues, {Murillo F.} and Kumar Saunack and Thibaut Sellinger and Kevin Thornton and {Van Kemenade}, Hugo and Wohns, {Anthony W.} and Yan Wong and Simon Gravel and Kern, {Andrew D.} and Jere Koskela and Ralph, {Peter L.} and Jerome Kelleher",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2021.",

year = "2022",

doi = "10.1093/genetics/iyab229",

language = "English",

volume = "220",

journal = "Genetics",

issn = "1943-2631",

publisher = "The Genetics Society of America (GSA)",

number = "3",

}

RIS

TY - JOUR

T1 - Efficient ancestry and mutation simulation with msprime 1.0

AU - Baumdicker, Franz

AU - Bisschop, Gertjan

AU - Goldstein, Daniel

AU - Gower, Graham

AU - Ragsdale, Aaron P.

AU - Tsambos, Georgia

AU - Zhu, Sha

AU - Eldon, Bjarki

AU - Ellerman, E. Castedo

AU - Galloway, Jared G.

AU - Gladstein, Ariella L.

AU - Gorjanc, Gregor

AU - Guo, Bing

AU - Jeffery, Ben

AU - Kretzschumar, Warren W.

AU - Lohse, Konrad

AU - Matschiner, Michael

AU - Nelson, Dominic

AU - Pope, Nathaniel S.

AU - Quinto-Cortes, Consuelo D.

AU - Rodrigues, Murillo F.

AU - Saunack, Kumar

AU - Sellinger, Thibaut

AU - Thornton, Kevin

AU - Van Kemenade, Hugo

AU - Wohns, Anthony W.

AU - Wong, Yan

AU - Gravel, Simon

AU - Kern, Andrew D.

AU - Koskela, Jere

AU - Ralph, Peter L.

AU - Kelleher, Jerome

PY - 2022

Y1 - 2022

N2 - 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, a large number of specialized 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 the tskit library. We summarize msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized 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.

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, a large number of specialized 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 the tskit library. We summarize msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized 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.

KW - Ancestral Recombination Graphs

KW - coalescent

KW - mutations

KW - Simulation

U2 - 10.1093/genetics/iyab229

DO - 10.1093/genetics/iyab229

M3 - Journal article

C2 - 34897427

AN - SCOPUS:85125682611

VL - 220

JO - Genetics

JF - Genetics

SN - 1943-2631

IS - 3

M1 - iyab229

ER -

ID: 307101168

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