A new imputation pipeline that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data decribed in the publication by Pook T, Nemri A, Gonzalez Segovia EG, Simianer H, Schoen CC (2021) Increasing calling accuracy, coverage, and read depth in sequence data by the use of haplotype blocks. PLOS Genetics, doi.org/10.1371/journal.pgen.1009944
https://github.com/tpook92/HBimpute
The R-scripts accompany the statistical framework described in detail in Mayer M, Hölker AC, González-Segovia E, Bauer E, Presterl T, Ouzunova M, Melchinger AE, Schön CC (2020) Discovery of beneficial haplotypes for complex traits in maize landraces. Nature Commun 11:4954, doi.org/10.1038/s41467-020-18683-3
https://github.com/Manfred-Mayer/GWAS_DHs_landraces
MoBPS is a framework to simulate, evaluate and compare breeding programs.
https://www.mobps.de/
https://github.com/tpook92/MoBPS
‘HaploBlocker’ is an R-package to compute a haplotype block library according to our paper by Pook T, Schlather M, de los Campos G, Schoen CC, Simianer H (2019) HaploBlocker: Creation of subgroup specific haplotype blocks and libraries. Genetics 212:1045-1061, doi.org/10.1534/genetics.119.302283
https://github.com/tpook92/HaploBlocker
Epistatic relationship matrix based genomic prediction of phenotypes.
https://github.com/evojgani/EpiGP
‘synbreed’ is an open-source R package for deriving genome-based predictions from high-throughput genotyping and large-scale phenotyping data. It contains a comprehensive collection of functions required to fit and crossvalidate genomic predictions models.
Wimmer V, Albrecht T, Auinger HJ, Schön CC (2012) synbreed: A framework for the analysis of genomic prediction data using R. Bioinformatics 28:2086-2087
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Technical University of Munich
Plant Breeding
plantbreeding.wzw@tum.de
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