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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #406795
Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: rTASSEL: An R interface to TASSEL for analyzing genomic diversity

Author
item MONIER, BRANDON - Cornell University
item CASSTEVENS, TERRY - Cornell University
item BRADBURY, PETER - Retired ARS Employee
item Buckler, Edward - Ed

Submitted to: Journal of Open Source Software
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/21/2022
Publication Date: 8/10/2022
Citation: Monier, B., Casstevens, T.M., Bradbury, P., Buckler IV, E.S. 2022. rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software. https://doi.org/10.21105/joss.04530.
DOI: https://doi.org/10.21105/joss.04530

Interpretive Summary: With the ever-growing amount of genomic data and resources, efficient and reproducible methods are needed for analysis. One such resource, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), was made available over a decade ago. While TASSEL provides powerful solutions for a variety of genomic questions, reproducibility and interactivity with other prominent analytical resources are lacking. Here, we present rTASSEL - an open-source software for accessing powerful TASSEL methods in the R computing environment. R provides the ability to (1) create straight-forward functionalities, (2) create reproducible analytical pipelines, (3) interact with many other prominent statistical and graphical libraries, and (4) operate in a user-friendly workspace.

Technical Abstract: 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 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.