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 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<jats:monospace>msprime</jats:monospace>version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and<jats:monospace>tskit</jats:monospace>library. We summarise<jats:monospace>msprime</jats:monospace>’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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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 08. Nov. Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| doi: |
10.1101/2021.08.31.457499 |
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| PPN (Katalog-ID): |
XBI032496664 |
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| 100 | 1 | |a Baumdicker, Franz |e verfasserin |0 (orcid)0000-0001-9106-7259 |4 aut | |
| 245 | 1 | 0 | |a Efficient ancestry and mutation simulation with msprime 1.0 |
| 264 | 1 | |c 2023 | |
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| 520 | |a 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 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<jats:monospace>msprime</jats:monospace>version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and<jats:monospace>tskit</jats:monospace>library. We summarise<jats:monospace>msprime</jats:monospace>’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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| 700 | 1 | |a Ragsdale, Aaron P. |0 (orcid)0000-0003-0715-3432 |4 aut | |
| 700 | 1 | |a Tsambos, Georgia |0 (orcid)0000-0001-7001-2275 |4 aut | |
| 700 | 1 | |a Zhu, Sha |0 (orcid)0000-0001-7566-2787 |4 aut | |
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| 700 | 1 | |a Matschiner, Michael |0 (orcid)0000-0003-4741-3884 |4 aut | |
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