Breeding Insight’s open source software solutions

These open source software solutions offer users a way to make various genomic, bioinformatic and phenomic workflows easier.

Any questions regarding any of our tools? Email breedinginsight@cornell.edu.

BIGr

BIGr is a RPackage for a-to-z genomic analyses.

Applications: Genomics, GWAS, GS

Language: R

Developers: Alexander Sandercock

GitHub link: https://github.com/Breeding-Insight/BIGr

RRID: SCR_o26677

For citations, please include both of the following for the package and the methods:

  • Sandercock, Alexander M., Cristiane H. Taniguti, Josue Chinchilla-Vargas, Dongyan Zhao, Shufen Chen, Meng Lin, Manoj Sapkota, and Breeding Insight Team. 2025. “Breeding Insight Genomics Functions for Polypoid and Diploid Species.”
  • Sandercock A.M., Peel M.D., Tanigut C.H., Chinchilla-Vargas J., Chen S., Sapkota M., Lin M., Zhao D., Ackerman A.J., Basnet B.R., Beil C.T., Sheehan M.J. (2025). BIGapp: A User-Friendly Genomic Tool Kit Identified Quantitative Trait Loci for Creeping Rootedness in Alfalfa (Medicago sativa L.)., The Plant Genome. doi:https://doi.org/10.1002/tpg2.70067
Qploidy

Qploidy is a RPackage tools for ploidy estimation with array and target markers.

Applications: Genomics

Language: R

Developers: Cris Taniguti

GitHub link: https://github.com/Cristianetaniguti/qploidy

RRID: SCR_o26724

For citations, please reference the following: Taniguti, C.H; Lau, J.; Hochhaus, T.; Arias Lopez, D. C.; Hokanson, S.C.; Zlesak, D. C.; Byrne, D. H.; Klein, P.E. and Riera-Lizarazu, O. Exploring Chromosomal Variations in Garden Roses: Insights from High-density SNP Array Data and a New Tool, Qploidy. The Plant Genome, e70044. https://doi.org/10.1002/tpg2.70044

 

BerryPortraits logo
BerryPortraits

BerryPortraits is a Python pipeline for image analysis.

Applications: Image analysis

Language: Python

Developers: Tyr Weisner-Hanks

GitHub link: https://github.com/Breeding-Insight/berryportraits

RRID: SCR_026628

For citations, please reference the following: Loarca, J., Wiesner-Hanks, T., Lopez-Moreno, H. et al. BerryPortraits: Phenotyping Of Ripening Traits in cranberry (Vaccinium macrocarpon Ait.) with YOLOv8. Plant Methods 20, 172 (2024). https://doi.org/10.1186/s13007-024-01285-1