TY - JOUR
T1 - dartR v2
T2 - An accessible genetic analysis platform for conservation, ecology and agriculture
AU - Mijangos, Jose Luis
AU - Gruber, Bernd
AU - Berry, Oliver
AU - Pacioni, Carlo
AU - Georges, Arthur
N1 - Funding Information:
This project and the scripts that are included were funded in part by a grant from the ACT Priority Investment Fund, the Cooperative Research Network for Murray‐Darling Basin Futures, the ARC Linkage Program, and the CSIRO Environomics Future Science Platform. Open access publishing facilitated by University of Canberra, as part of the Wiley ‐ University of Canberra agreement via the Council of Australian University Librarians.
Funding Information:
This project and the scripts that are included were funded in part by a grant from the ACT Priority Investment Fund, the Cooperative Research Network for Murray-Darling Basin Futures, the ARC Linkage Program, and the CSIRO Environomics Future Science Platform. Open access publishing facilitated by University of Canberra, as part of the Wiley - University of Canberra agreement via the Council of Australian University Librarians.
Publisher Copyright:
© 2022 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.
PY - 2022/6/11
Y1 - 2022/6/11
N2 - 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. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
AB - 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. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
KW - conservation genetics
KW - DArT
KW - next-generation sequencing
KW - R
KW - single nucleotide polymorphism
UR - http://www.scopus.com/inward/record.url?scp=85133897172&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.13918
DO - 10.1111/2041-210X.13918
M3 - Article
AN - SCOPUS:85133897172
SN - 2041-210X
VL - 13
SP - 2150
EP - 2158
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
IS - 10
ER -