XSim
XSim is a fast and user-friendly tool to simulate sequence data and complicated pedigree structures
- Homepage: QTL.rocks
- Discussion group: available here
- Installation: at the Julia REPL,
using Pkg; Pkg.add("XSim") - Documentation: available here
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)
# 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.