ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process.
Simulation under the coalescent model is ubiquitous in the analysis of genetic data. The rapid growth of real data sets from multiple human populations led to increasing interest in simulating very large sample sizes at whole-chromosome scales. When the sample size is large, the coalescent model becomes an increasingly inaccurate approximation of the discrete time Wright-Fisher model (DTWF). Analytical and computational treatment of the DTWF, however, is generally harder.



We present a simulator (ARGON) for the DTWF process that scales up to hundreds of thousands of samples and whole-chromosome lengths, with a time/memory performance comparable or superior to currently available methods for coalescent simulation. The simulator supports arbitrary demographic history, migration, Newick tree output, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identical-by-descent sharing data.



ARGON (version 0.1) is written in Java, open source, and freely available at https://github.com/pierpal/ARGON CONTACT: ppalama@hsph.harvard.edu



Supplementary data are available at Bioinformatics online.
Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Pier Francesco
PF
Palamara
D000818:Animals; D003198:Computer Simulation; D005785:Gene Conversion; D016678:Genome; D006801:Humans; D008962:Models, Theoretical; D009154:Mutation