RT Journal Article
SR Electronic
T1 rTASSEL: an R interface to TASSEL for association mapping of complex traits
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.07.21.209114
DO 10.1101/2020.07.21.209114
A1 Monier, Brandon
A1 Casstevens, Terry M.
A1 Bradbury, Peter J.
A1 Buckler, Edward S.
YR 2021
UL http://biorxiv.org/content/early/2021/03/31/2020.07.21.209114.abstract
AB Summary The need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited means to use scripting languages for reproducible research and interacting with other analytical tools. Here we present an R package rTASSEL, a front-end to connect to a variety of highly used TASSEL methods and analytical tools. The goal of this package is to create a unified scripting workflow that exploits the analytical prowess of TASSEL in conjunction with R’s popular data handling and parsing capabilities without ever having the user to switch between these two environments. By implementing this workflow, we can achieve performances ranging from approximately 2 to 20 times faster than other widely used R packages for various functionalities.Availability and implementation rTASSEL is implemented in R using core TASSEL methods written in Java. The source code for rTASSEL can be found at https://bitbucket.org/bucklerlab/rtassel/src/master/. The source code for TASSEL can be found at https://bitbucket.org/tasseladmin/tassel-5-source/src/master/.Supplemental information The rTASSEL user manual and tutorials are freely available at https://maize-genetics.github.io/rTASSEL/. Supplemental material for this manuscript regarding performance metrics can be found in the attached file.Competing Interest StatementThe authors have declared no competing interest.