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XSim

simulate sequence data and complicated pedigree structures

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XSim

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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.

First Commit

02/13/2015

Last Touched

5 months ago

Commits

130 commits

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