Efficient ancestry and mutation simulation with msprime 1.0.
Efficient ancestry and mutation simulation with msprime 1.0.
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DOI：
10.1093/genetics/iyab229
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发表时间：
2022-03-03
期刊：
影响因子：
3.3
通讯作者：
Kelleher, Jerome
中科院分区：
文献类型：
--
作者：
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
随机模拟是群体遗传学中的一个关键工具，因为所涉及的模型通常在分析上是难以处理的，并且模拟通常是获得地面实况数据以评估推断的唯一方法。正因为如此，大量专门的模拟程序已经开发出来，每一个填补了一个特定的利基，但在很大程度上重叠的功能和大量的重复工作。在这里，我们介绍msprime版本1.0，它有效地实现了祖先和突变模拟的基础上简洁的树序列数据结构和tskit库。我们总结了msprime的许多功能，并表明它的性能是优秀的，往往比专门的替代品快很多倍，更内存效率。这些高性能功能已经过全面测试和验证，并使用协作式开源开发模型构建，通过社区参与减少重复工作并提高软件质量。自2016年推出以来，msprime模拟器越来越受欢迎，现在是群体遗传学中最常用的工具之一。本文标志着msprime的1.0发行版，并总结了它通过开放源码社区开发模型积累的许多特性。尽管msprime具有通用性，但它的性能非常出色在许多情况下，它比更专门的方法快几个数量级，而且更节省内存。
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. Since its introduction in 2016, the msprime simulator has grown in popularity and is now one of the most commonly used tools in population genetics. This article marks the 1.0 release of msprime and summarizes the many features it has accumulated through an open source community development model. Despite its generality, msprime’s performance is excellent—in many cases orders of magnitude faster and more memory efficient than more specialized methods.
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