Rhometa: Population recombination rate estimation from metagenomic read datasets

Bacterial evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a bacterial population. We introduce Rhometa (), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes.It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. In simulated datasets, the deviation from the expected value decreased as the number of genomes increased and we show that 80 genomes are sufficient to reduce these variations below 30%. Testing on an S. pneumoniae transformation experiment dataset we show that Rhometa accurately estimate the expected levels of recombination in a real world dataset. ### Competing Interest Statement A. E. Darling holds equity in Illumina Inc and is employed by its subsidiary Illumina Australia Pty Ltd, a company that develops and sells DNA sequencing technology. All other authors declare no competing financial interests.