pierrepeterlongo / haplosim

Simulate haplotypes according to a random markovian chain along a binary evolutionnary tree and generate metagenomic illumina data from a random admixture of simulated haplotypes

haploSim

haploSim contains a couple of python scripts to

1. simulate haplotypes according to a random markovian chain along a binary evolutionnary tree (simHaplo.py)
2. generate metagenomic illumina data from a random admixture of simulated haplotypes (simMetaG.py)
3. compute the pairwise (simHaplo.py) and global (simMetaG.py) nucleotide diversity (π)

Quick example on Coronavirus

This example simulates 16 haplotypes with default settings and generates illumina reads

python3 simHaplo.py -i wuhan-hu1.fasta -o CoronaHaplo -s 16
python3 simMetaG.py -i CoronaHaplo -o  Corona_1_reads -n 10

How to simulate haplotypes?

To simulate haplotypes, use the simHaplo.py script. Several parameters can be tuned as follow:

simHaplo.py -i inputFasta -o outputDir -k varFreq -r recombFreq -s strainsNumber -n haploNumber

   -i input directory that contains fasta file
   -o output directory
   -k variant frequency (default 0.01)
   -d variant frequency dispersion (default 0.001)
   -r recombination frequency (default 0.0001)
   -s number of initial strains to generate (default 16)
   -n number of haplotypes to generate (default 10)
   -m minimum abundance of a haplotype (default 10x)

How to simulate metagenomic reads from a haplotypes admixture?

Once the haplotypes have been created, use simMetaG to generate illumina reads on a random admixture of haplotypes. You need the wgsim program (part of samtools) in you $PATH. Several parameters can tuned as follow:

 simMetaG.py -i inputHaplo -o outputDir -n haploNumber

   -i input directory that contains haplotypes fasta files
   -o output directory
   -n minimum of haplotypes per species (default 5)
   -l read leangth (default 100)
   -m minimum abundance of an haplotype (default 10x)