Rhometa: Population recombination rate estimation from metagenomic read datasets.

ABSTRACT: Prokaryotic 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 prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/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. Rhometa offers a comprehensive solution for determining population recombinatio

SUBMITTER: Krishnan S 

PROVIDER: S-EPMC10079220 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature