XSim.jl: Simulate Sequence Data & Complicated Pedigree Structures

XSim

XSim is a fast and user-friendly tool to simulate sequence data and complicated pedigree structures

Features

An efficient CPOS algorithm
Using founders that are characterized by real genome sequence data
Complicated pedigree structures among descendants

Quick-start

# Load XSim
using XSim

# Simulate genome with 10 chromosomes, and 100 markers are located on each chromosome.
build_genome(n_chr=10, n_loci=100)
# Simulate two independent traits controlled by 3 and 8 QTLs, respectively.
build_phenome([3, 8])

# Initialize founders
n_sires = 3
n_dams  = 20
sires   = Founders(n_sires)
dams    = Founders(n_dams)

# Define parameters
args     = Dict(# mating
                :nA               => 3,
                :nB_per_A         => 5,
                :n_per_mate       => 2,
                :ratio_malefemale => 1.0,
                # selection
                :h2               => [.8, .5],
                :weights          => [.6, .4],
                # breeding
                :n_gens           => 5,
                :n_select_A       => 3,
                :n_select_B       => 20)

# Breeding program
sires_new, dams_new   = breed(sires, dams; args...)

# Inspect the results
summary(sires + dams)
summary(sires_new + dams_new)

Citing XSimV2

Bibliography

Chen, C.J., D. Garrick, R. Fernando, E. Karaman, C. Stricker, M. Keehan, and H. Cheng. 2022. XSim version 2: simulation of modern breeding programs. G3 Genes|Genomes|Genetics 12:jkac032. doi:10.1093/g3journal/jkac032.

BibTeX

@article{chen_xsim_2022,
 title = {{XSim} version 2: simulation of modern breeding programs},
 volume = {12},
 issn = {2160-1836},
 url = {<https://doi.org/10.1093/g3journal/jkac032>},
 doi = {10.1093/g3journal/jkac032},
 number = {4},
 urldate = {2022-05-26},
 journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
 author = {Chen, Chunpeng James and Garrick, Dorian and Fernando, Rohan and Karaman, Emre and Stricker, Chris and Keehan, Michael and Cheng, Hao},
 month = apr,
 year = {2022},
}

Help

Old users may install the old version of XSim as using Pkg; Pkg.add(name="XSim", version="0.5")

Authors: Hao Cheng,Rohan Fernando,Dorian Garrick
Citing XSim

Cheng H, Garrick D, and Fernando R (2015) XSim: Simulation of descendants from ancestors with sequence data. G3: Genes-Genomes-Genetics, 5(7):1415-1417.

Homepage: QTL.rocks
Discussion group: available here
Installation: at the Julia REPL, using Pkg; Pkg.add("XSim")
Documentation: available here

Download Details:

Author: Reworkhow
Source Code: https://github.com/reworkhow/XSim.jl
License: GPL-2.0 license

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