2022
DOI: 10.1111/2041-210x.13918
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dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Abstract: 1. Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/ absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dart… Show more

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Cited by 87 publications
(51 citation statements)
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“…The chickpea SNP data set [ 23 ] was provided in HapMap format and was converted to VCF format using TASSEL 5 Standalone ([ 29 ]; see the processing pipeline described in Supplementary Materials D3 Additional File. Hexaploid, tetraploid, and wild wheat SNP data files [ 22 ] were provided in DArT format [ 30 ]. These files were subdivided based on the provided passport information, with monomorphic loci removed, and then converted directly to GBS format, retaining only bi-allelic SNP loci, using the dartR R package (See the processing procedures described in Supplementary Materials D2 Additional File).…”
Section: Methodsmentioning
confidence: 99%
“…The chickpea SNP data set [ 23 ] was provided in HapMap format and was converted to VCF format using TASSEL 5 Standalone ([ 29 ]; see the processing pipeline described in Supplementary Materials D3 Additional File. Hexaploid, tetraploid, and wild wheat SNP data files [ 22 ] were provided in DArT format [ 30 ]. These files were subdivided based on the provided passport information, with monomorphic loci removed, and then converted directly to GBS format, retaining only bi-allelic SNP loci, using the dartR R package (See the processing procedures described in Supplementary Materials D2 Additional File).…”
Section: Methodsmentioning
confidence: 99%
“…Principal Components Analysis was undertaken using the glPCA function of the R adegenet package (as implemented in dartR, Gruber et al, 2018; Jombart, 2008; Jombart & Ahmed, 2011). Principal Coordinates Analysis was undertaken using the pcoa function in R package ape (Paradis & Schliep, 2019) implemented in dartR Version 2 (Mijangos et al, 2022).…”
Section: Methodsmentioning
confidence: 99%
“…The algorithms discussed in this paper form the basis of the distance analysis implemented in R software package dartR (Gruber et al, 2018; Mijangos et al, 2022).…”
Section: Methodsmentioning
confidence: 99%
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