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 micro-epidemics 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 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. Supplementary data are available at Bioinformatics online.
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Jan 27, 2019·Genome Research·John A LeesNicholas J Croucher
Feb 27, 2020·Microbial Genomics·Morteza M Saber, B Jesse Shapiro
Jun 26, 2020·BMC Bioinformatics·Louis-Marie Bobay
Sep 29, 2021·PLoS Genetics·Jessica K CallandSamuel K Sheppard