Rhometa

Rhometa estimates population recombination rates in prokaryotic populations from short-read metagenomic datasets.

Key Features:

• Composite Likelihood Approach: Extends traditional sequence-based composite likelihood methods to accommodate short-read metagenomic datasets for recombination rate estimation.
• Compatibility with Modern Sequencing Data: Handles diverse sequencing depths and is tailored for contemporary shotgun short-read sequencing data.
• Validation and Accuracy: Evaluated on simulated and real experimental data with accuracy improving as the number of genomes in the dataset increases.

Scientific Applications:

• Metagenomic Analysis: Enables estimation of recombination rates from metagenomic datasets, including data from uncultured environments such as ocean surface waters.
• Prokaryotic Evolution Studies: Provides recombination rate estimates to inform studies of evolutionary dynamics and adaptive potential in prokaryotic communities.

Methodology:

Implements an advanced composite likelihood framework to analyze aligned metagenomic read datasets; tested across a range of sequencing depths and complexities and validated using a Streptococcus pneumoniae transformation experiment.