A community-maintained standard library of population genetic models

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Re-cent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a pa...

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Bibliographic Details
Main Authors: Adrion, JR, Cole, CB, Dukler, N, Galloway, JG, Gladstein, AL, Gower, G, Kyriazis, CC, Ragsdale, AP, Tsambos, G, Baumdicker, F, Carlson, J, Cartwright, RA, Durvasula, A, Gronau, I, Kim, BY, McKenzie, P, Messer, PW, Noskova, E, Ortega Del Vecchyo, D, Racimo, F, Struck, TJ, Gravel, S, Gutenkunst, RN, Lohmueller, KE, Ralph, PL, Schrider, DR, Siepel, A, Kelleher, JT, Kern, AD
Format: Journal article
Language:English
Published: eLife Sciences Publications 2020
Description
Summary:The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Re-cent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.