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 package
using XSim
#set genome information
chrLength= 0.1 #length of each chromosome
numChr = 2 #number of chromosomes
nLoci = 10 #number of loci for each chromosome
nQTL = 1 #number of QTL for each chromosomefects,mutRate);
build_genome(numChr,chrLength,nLoci,nQTL) #this genome information will be used for subsequent computaions
#generate founders
popSizeFounder = 2
sires = sampleFounders(popSizeFounder);
dams = sampleFounders(popSizeFounder);
#random mating
ngen,popSize = 5,10
sires1,dams1,gen1 = sampleRan(popSize, ngen, sires, dams);More
- homepage: QTL.rocks
- Installation: at the Julia REPL,
Pkg.add("XSim") - Documentation: available here
- 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.