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ABHgenotypeR

ABHgenotypeR

ABHgenotypeR is an R tool for genotype imputation, error correction, and plotting genotype data. The purpose of ABHgenotypeR is to work as an in-between tool for TASSEL GBS pipeline and qtl tool. However, ABHgenotypeR is an independent tool and can visualize genotypes using ggplot2.

Topic

Population genetics

Details

  • Operation: Visualisation; Imputation
  • Input: ABH-based format, where A represents NB, B represents OL, and H represents heterozygous alleles.
  • Output: -
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.0.1
  • Maturity: Stable
  • Credit: Core Research for Evolutional Science and Technology, the Japan Science and Technology Agency, he Council for Science, Technology and Innovation, Cross-ministerial Strategic Innovation Promotion Program, Technologies for creating next-generation agriculture, forestry and fisheries, Bio-oriented Technology Research Advancement Institution (NARO), National Bio Resource Project (NBRP) Rice."
  • Contact: Stefan Reuscher reuscher.stefan _at_ gmail.com
  • Collection: -

Publications

Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S "Adapting Genotyping-by-Sequencing for Rice F2 Populations." G3 (Bethesda). 2017 Mar 10;7(3):881-893. https://doi.org/10.1534/g3.116.038190
PMID: 28082325
PMCID: PMC5345719

Download and documentation


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