Computational Methods in Microbial Population Genomics
Whole genome sequencing is frequently applied to hundreds of samples within a single microbial population study. The resulting datasets are large and need to be analysed using computationally efficient methods, the development of which is an active research field. Here we review the current state of the art in terms of computation methods used in microbial population genomics. This includes software for assembly and alignment of core genomic regions, which is usually a pre-requirement for analysing the ancestry of the genomes, via phylogenetic on non-phylogenetic methods. We also review additional techniques aimed at combining genomic data with temporal, geographical or other types of metadata, as well as pan-genome methods of analysis that go beyond the core genome.
KeywordsAlignment Assembly Computation methods Microbial population genomics Pan-genome analysis Phylodynamics Phylogenetics Phylogeography Recombination
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