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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

genepopedit: a simple and flexible tool for manipulating multilocus molecular data in R.

Ryan R E Stanley^1,2, Nicholas W Jeffery³, Brendan F Wringe^1,3

¹Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada.

Molecular Ecology Resources

|July 20, 2016

Summary

Researchers can now easily manage large genomic datasets with genepopedit, a new R package. This tool simplifies data manipulation and conversion for population genetics analyses, even with millions of single nucleotide polymorphisms (SNPs).

Keywords:

R statistics conservation genetics data conversion data manipulation loci selection population genetics

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Area of Science:

Genomics
Bioinformatics
Population Genetics

Background:

Genetic sequencing advances generate large, complex genome-wide datasets.
Handling these large datasets poses computational challenges for researchers.
Existing tools may not efficiently manage multilocus molecular data for nonmodel organisms.

Purpose of the Study:

To develop a flexible tool for manipulating multilocus molecular datasets.
To address computational challenges in processing large genomic data.
To facilitate population structure and demographic analyses.

Main Methods:

Developed genepopedit as an R package.
Included diagnostic, manipulation, sampling, simulation, and transformation tools.
Enabled efficient metadata extraction and data conversion to various software formats.

Main Results:

genepopedit efficiently handles large genomic datasets, including those exceeding 200,000 SNPs.
The tool simplifies manipulation of loci, individual samples, and populations.
It integrates seamlessly into existing R-based analysis workflows.

Conclusions:

genepopedit offers a robust, code-based solution for repeatable genomic data manipulation.
The package enhances the analysis of population structure and demographic processes.
It supports researchers working with large-scale genomic data from nonmodel organisms.