Citation

If Binx is useful in your research, please cite both the original methods and the Binx implementation.

Citing Binx

Sandercock, A.M. (2025). Binx: A Rust-based CLI tool for polyploid and diploid 
genomic analysis. GitHub repository: https://github.com/alex-sandercock/Binx

BibTeX:

@software{sandercock2025binx,
  author = {Sandercock, Alexander M.},
  title = {Binx: A Rust-based CLI tool for polyploid and diploid genomic analysis},
  year = {2025},
  url = {https://github.com/alex-sandercock/Binx}
}

Note: A formal publication with DOI is planned. This section will be updated when available.

Citing the Methods

rrBLUP (Mixed Model)

If using the GWAS or kinship functionality:

Endelman, J.B. (2011). Ridge regression and other kernels for genomic selection 
with R package rrBLUP. The Plant Genome 4:250-255.

@article{endelman2011rrblup,
  author = {Endelman, Jeffrey B.},
  title = {Ridge regression and other kernels for genomic selection with R package rrBLUP},
  journal = {The Plant Genome},
  volume = {4},
  pages = {250--255},
  year = {2011},
  doi = {10.3835/plantgenome2011.08.0024}
}

GWASpoly (Polyploid GWAS)

If using polyploid genetic models:

Rosyara, U.R., De Jong, W.S., Douches, D.S., & Endelman, J.B. (2016). Software 
for genome-wide association studies in autopolyploids and its application to 
potato. The Plant Genome 9(2).

@article{rosyara2016gwaspoly,
  author = {Rosyara, Umesh R. and De Jong, Walter S. and Douches, David S. and Endelman, Jeffrey B.},
  title = {Software for genome-wide association studies in autopolyploids and its application to potato},
  journal = {The Plant Genome},
  volume = {9},
  number = {2},
  year = {2016},
  doi = {10.3835/plantgenome2015.08.0073}
}

Updog (Dosage Estimation)

If using the dosage estimation functionality:

Gerard, D., Ferrão, L.F.V., Garcia, A.A.F., & Stephens, M. (2018). Genotyping 
polyploids from messy sequencing data. Genetics 210(3):789-807.

@article{gerard2018updog,
  author = {Gerard, David and Ferrão, Luis Felipe Ventorim and Garcia, Antonio Augusto Franco and Stephens, Matthew},
  title = {Genotyping polyploids from messy sequencing data},
  journal = {Genetics},
  volume = {210},
  number = {3},
  pages = {789--807},
  year = {2018},
  doi = {10.1534/genetics.118.301468}
}

Example Acknowledgment

In your methods section:

GWAS was performed using Binx v0.1.0 (Sandercock, 2025), which implements the GWASpoly framework (Rosyara et al., 2016) and rrBLUP mixed model (Endelman, 2011) in Rust. Multiple genetic models were tested including additive and general models appropriate for autotetraploid inheritance.

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