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rTASSEL: an R interface to TASSEL for association mapping of complex traits

View ORCID ProfileBrandon Monier, View ORCID ProfileTerry M. Casstevens, View ORCID ProfilePeter J. Bradbury, View ORCID ProfileEdward S. Buckler
doi: https://doi.org/10.1101/2020.07.21.209114
Brandon Monier
1Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • For correspondence: brandon.monier@gmail.com
Terry M. Casstevens
1Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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Peter J. Bradbury
1Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
2United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Edward S. Buckler
1Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
2United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • Contact bm646{at}cornell.edu

  • Reduced wording and added performance metrics of various functionalities in supplemental information.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 31, 2021.
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rTASSEL: an R interface to TASSEL for association mapping of complex traits
Brandon Monier, Terry M. Casstevens, Peter J. Bradbury, Edward S. Buckler
bioRxiv 2020.07.21.209114; doi: https://doi.org/10.1101/2020.07.21.209114
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rTASSEL: an R interface to TASSEL for association mapping of complex traits
Brandon Monier, Terry M. Casstevens, Peter J. Bradbury, Edward S. Buckler
bioRxiv 2020.07.21.209114; doi: https://doi.org/10.1101/2020.07.21.209114

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