Dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. (15th January 2018)

• Record Type: Journal Article
• Authors: Gruber, Bernd; Unmack, Peter J.; Berry, Oliver F.; Georges, Arthur
• Is Part Of: Molecular ecology resources. Volume 18:Number 3(2018:May)
• Page Start: 691
• Page End: 699
• Publication Date: 2018-01-15
• Subjects: next‐generation sequencing -- phylogenomics -- population genomics -- r package -- RADSeq -- SNPs; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12745
• Languages: English
• ISSNs: 1755-098X

Abstract

Abstract: Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a newr package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications.dartr provides user‐friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy–Weinberg equilibrium, gametic‐phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F‐statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of ther environment. The package serves two main purposes: first, a user‐friendly approach to lower the hurdle to analyse such data—therefore, the package comes with a detailed tutorial targeted to ther beginner to allow data analysis without requiring deep knowledge ofr . Second, we use a single, well‐established format—genlight from theadegenet package—as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. Thedartr package is available via ther CRAN network and GitHub.