Zachary Winn's repositories
HAPLOCATCHER-AN-R-PACKAGE-FOR-PREDICTION-OF-HAPLOTYPES
A data and code repository for the paper of the same name.
HPC-GBS-Pipeline
This is a set of scripts to implement the TASSEL 5 Standalone pipeline on the SCINet HPC system.
Mapping-of-a-Novel-Major-Effect-Hessian-Fly-Partial-Resistance-Locus-in-Southern-SRWW-LA03136E71
Data repository for the paper of the same name.
Phenomic-vs-GP-A-Comparison-of-Prediction-Accuracies-for-GY-in-HWW
This is a public repository for relevant code from the publication of the same name.
TASSEL-VCF-Fixer
A program for fixing TASSEL produced GBS VCFs so that they are coded reference-alternate
HaploCatcher
An R package for inferring Haplotypes from high-density, non-targeted genotyping platforms
KlusterCaller-to-VCF
Modify KASP assay calls to a VCF format
MAS-Summary-Script
An R script for parsing VCFs into MAS reports for wheat breeders on the east coast of the US
MVGS-improves-GP-Accuracy-in-SRWW
This is a public repository for relevant code from the publication of the same name.
NC13-20076-FHB-QTL-Mapping
A data repository related to the paper "Genetic Mapping of Resistance To Fusarium Head Blight In Soft Red Winter Wheat Line NC13-20076"
Phenotyping-Anther-Extrusion-of-Wheat-Using-Image-Analysis
Repository for MDPI Paper in 2021
Profiling-of-FHB-Resistance-QTL-Haplotypes-Through-MM-GBG-and-ML
This is the data repository for the publication of the same name.
SNP-Sequence-Puller
A program for pulling flanking sequences from a reference genome for a SNP
Utilization-of-a-Publicly-Available-Diversity-Panel-in-GP-of-FHB-Resistance-Traits-in-Wheat
This is a public repository for relevant code from the publication of the same name.
Winn-Dissertation-Chapter-3
This is the public repository for information related to the thesis chapter of the same name as the title.
Winn-Dissertation-Chapter-4
This is the public repository for information related to the thesis chapter of the same name as the title.
Yield-Protection-Afforded-By-Imidaclorpid-During-HF-Infestation-In-Six-Backgrounds
This is a public data repository for data related to a publication.
SNP_Primer_Pipeline2
Design gene specific KASP and CAPS/dCAPS primers for any species
wheat-assembly
The repository contains scripts for wheat genome assembly of PacBio CCS reads.
Wheat-KASP-Designer
This is a repository designed to take a VCF and reference genome and design potential KASP assays
wheat-te-annotation
This pipeline uses repeatmasker, repeatmodeler, and the TREP database (https://trep-db.uzh.ch/) to annotate and mask transposable elements (TEs) in a wheat genome assembly.