RT Journal Article
SR Electronic
T1 Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.10.29.514266
DO 10.1101/2022.10.29.514266
A1 M. Elise Lauterbur
A1 Maria Izabel A. Cavassim
A1 Ariella L. Gladstein
A1 Graham Gower
A1 Nathaniel S. Pope
A1 Georgia Tsambos
A1 Jeff Adrion
A1 Saurabh Belsare
A1 Arjun Biddanda
A1 Victoria Caudill
A1 Jean Cury
A1 Ignacio Echevarria
A1 Benjamin C. Haller
A1 Ahmed R. Hasan
A1 Xin Huang
A1 Leonardo Nicola Martin Iasi
A1 Ekaterina Noskova
A1 Jana Obšteter
A1 Vitor Antonio Corrêa Pavinato
A1 Alice Pearson
A1 David Peede
A1 Manolo F. Perez
A1 Murillo F. Rodrigues
A1 Chris C. R. Smith
A1 Jeffrey P. Spence
A1 Anastasia Teterina
A1 Silas Tittes
A1 Per Unneberg
A1 Juan Manuel Vazquez
A1 Ryan K. Waples
A1 Anthony Wilder Wohns
A1 Yan Wong
A1 Franz Baumdicker
A1 Reed A. Cartwright
A1 Gregor Gorjanc
A1 Ryan N. Gutenkunst
A1 Jerome Kelleher
A1 Andrew D. Kern
A1 Aaron P. Ragsdale
A1 Peter L. Ralph
A1 Daniel R. Schrider
A1 Ilan Gronau
YR 2022
UL http://biorxiv.org/content/early/2022/10/31/2022.10.29.514266.abstract
AB Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al.,2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.Competing Interest StatementThe authors have declared no competing interest.