Bacmeta: simulation for genomic evolution in bacterial metapopulations

Abstract

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and microepidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population, and ultimately the whole metapopulation, is efficiently simulated using C++ objects, and detailed metadata from each level of the simulation can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g., large-scale simulations and likelihood-free inference. Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license.\n\nContactaleksi.sipola@helsinki.fi,\n\njukka.corander@medisin.uio.no\n\nSupplementary informationSupplementary data are available online at bioRxiv.