PanGenomeSim

Simulate bacterial pangenomes according to the 'infinitely many genes' model and corresponding sequences using Jukes-Cantor.

Installation

Download the latest release. Then unpack and continue with the following steps.

autoreconf -fi  # optional when building from release tarball
./configure
make
make install  # optional, may require sudo

Verify that the installation was successful by running the following.

pangenomesim --help

This will give you a list of available options and parameters.

Usage

pangenomesim --out-dir sim

A new directory sim will be created and filled with various files. If no directory parameter was given, the current directory will be populated.

• ref.fasta: A technical reference genome for simulation; Union of core and accessory genes.
• genome*.fasta: The individual simulated bacterial genomes.
• accessory.fasta: The dispensable part of the reference genome.
• core.fasta: Genes shared by all genomes.
• alignment.maf: Sequence alignment of all genes.
• coalescent.newick: Evolutionary history of the genomes.
• distance.mat: Matrix of evolutionary distances.
• genefrequency.gfs: Distribution of gene frequencies.
• reproducible.seed: Parameters to reproduce this simulation.

Different parameters can be used to change the simulation. Use -p KEY=VALUE or --param KEY=VALUE to set a new value.

• core-size: Simulate additional core genes.
• gene-length: Set the length of a gene.
• mut-rate: Change the nucleotide substitution rate.
• num-genomes: Set the total number of genomes.
• rho: Rate of gene loss; See IMG model.
• seed: Seed for RNG.
• theta: Rate of gene gain; See IMG model.

The following two calls are equivalent.

pangenomesim --out-dir sim -p core-size=10 --param gene-length=2000
pangenomesim -o sim -p core-size=10,gene-length=2000

References

IMG Model

License

BSD 2-Clause License

Copyright (c) 2017, Fabian Klötzl [email protected]

See the License file for full detail.