Simulating Bacterial Population

Question

[Sama]

Is there any software available for simulating a bacterial population which contains similar strains?

Answer 1

[Brian Bushnell]

I am currently doing some simulations where I need bacterial populations at varying levels of identity to each other, so I wrote a tool to do that in the BBMap package. For example, using E.coli:

mutate.sh in=e_coli.fasta out=mutant.fasta id=99
randomreads.sh ref=mutant.fasta out=reads.fq.gz reads=5m length=150 paired adderrors

That will create a mutant version of E.coli with 99% identity to the original, and then generate 5 million simulated read pairs from the new genome. You can repeat this multiple times; each mutant will be different.

Answer 2

[natasha.sernova]

See these papers:

Assessing the reliability of eBURST using simulated populations with known ancestry

http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-7-30

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670731/

SimBac: simulation of whole bacterial genomes with homologous recombination

http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000044

Modeling Bacterial Population Growth from Stochastic Single-Cell Dynamics

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136116/

Also this one:

https://labs.wsu.edu/populationgenomics/resources/software-simulation-code/

There are many of them. The choice depends upon what exactly you need.