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Simulation of bacterial populations with SLiM

Jean Cury 1, 2 Benjamin C Haller 3 Guillaume Achaz 4, 5 Flora Jay 1, 2 
1 TAU - TAckling the Underspecified
Inria Saclay - Ile de France, LISN - Laboratoire Interdisciplinaire des Sciences du Numérique
2 BioInfo - BioInformatique
LISN - Laboratoire Interdisciplinaire des Sciences du Numérique, SDD - Science des Données
Abstract : Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiM’s scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.
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https://hal.archives-ouvertes.fr/hal-03152153
Contributor : Flora Jay Connect in order to contact the contributor
Submitted on : Thursday, January 13, 2022 - 12:02:14 PM
Last modification on : Friday, August 5, 2022 - 9:27:35 AM

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Jean Cury, Benjamin C Haller, Guillaume Achaz, Flora Jay. Simulation of bacterial populations with SLiM. Peer Community Journal, Peer Community In/Centre Mersenne, 2022, ⟨10.24072/pcjournal.72⟩. ⟨hal-03152153v3⟩

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