Bacmeta: Simulator for genomic evolution in bacterial metapopulations

Research output: Contribution to journalArticleScientificpeer-review

Researchers

Research units

  • University of Helsinki
  • University of Oslo

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.

Details

Original languageEnglish
Pages (from-to)2308-2310
Number of pages3
JournalBioinformatics
Volume34
Issue number13
Publication statusPublished - 1 Jul 2018
MoE publication typeA1 Journal article-refereed

ID: 27134379