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.
Input: ABH-based format, where A represents NB, B represents OL, and H represents heterozygous alleles.
Command-line user interface; Library
Operating system: Microsoft Windows, Mac OS X, Linux
GNU GPL v3
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."
Stefan Reuscher reuscher.stefan _at_ gmail.com
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
Download and documentation
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