LinkImpute
LinkImpute implements the LD-kNNi algorithm described in the following publication: Money D, Gardner KM, Migicovsky Z, Schwaninger H, Zhong GY, Myles S (2015) LinkImpute – fast and accurate genotype imputation for non-model organisms. G3: Genes, Genomes, Genetics 5:2383 [PubMed:26377960]
LinkImpute.tar.gz – program and manual.
LinkImpute-src.tar.gz – program, manual, source code and code documentation.
Inquiries about this software should be made to daniel.money@dal.ca
LinkImputeR
LinkImputeR calls and imputes genotypes from next-generation DNA sequence data using .vcf files as input. It is particularly well suited for non-model organisms with few genomic resources since it requires neither ordered markers nor a reference panel of genotypes. This software package is described in the following publication: Money D, Migicovsky Z, Gardner KM, Myles S (submitted) LinkImputeR: user-guided genotype calling and imputation for non-model organisms
LinkImputeR.tar.gz - program and manual
LinkImputeR-src.tar.gz - program, manual, source code and code documentation.
Inquiries about this software should be made to daniel.money@dal.ca
Resampling procedure in R
The following link provides the R script and the associated files used to determine the effect of sample size on the ability to map the Mendelian locus responsible for white/blue colour in F1 hybrid grapevine offspring. This file is referred to in the following manuscript: Myles S, Mahanil S, Harriman J, Gardner KM, Franklin JL, Reisch BI, Ramming DW, Owens CL, Li L, Buckler ES, Cadle-Davidson L (2015) Genetic mapping in grapevine using SNP microarray intensity values. Molecular Breeding (2015) Molecular Breeding 35:88.
myles_mol_breeding_Rscript.zip – R script and associated files
Python script to parse Genotyping-By-Sequencing data
The following link provides the Python code used to perform quality trimming and barcode deconvolution using Genotyping-By-Sequencing (GBS) data. The files are referred to in the following manuscript: Gardner et al. (in preparation) The genetic structure of the apple.
pythonscript.zip - Python scripts and libraries
LinkImpute implements the LD-kNNi algorithm described in the following publication: Money D, Gardner KM, Migicovsky Z, Schwaninger H, Zhong GY, Myles S (2015) LinkImpute – fast and accurate genotype imputation for non-model organisms. G3: Genes, Genomes, Genetics 5:2383 [PubMed:26377960]
LinkImpute.tar.gz – program and manual.
LinkImpute-src.tar.gz – program, manual, source code and code documentation.
Inquiries about this software should be made to daniel.money@dal.ca
LinkImputeR
LinkImputeR calls and imputes genotypes from next-generation DNA sequence data using .vcf files as input. It is particularly well suited for non-model organisms with few genomic resources since it requires neither ordered markers nor a reference panel of genotypes. This software package is described in the following publication: Money D, Migicovsky Z, Gardner KM, Myles S (submitted) LinkImputeR: user-guided genotype calling and imputation for non-model organisms
LinkImputeR.tar.gz - program and manual
LinkImputeR-src.tar.gz - program, manual, source code and code documentation.
Inquiries about this software should be made to daniel.money@dal.ca
Resampling procedure in R
The following link provides the R script and the associated files used to determine the effect of sample size on the ability to map the Mendelian locus responsible for white/blue colour in F1 hybrid grapevine offspring. This file is referred to in the following manuscript: Myles S, Mahanil S, Harriman J, Gardner KM, Franklin JL, Reisch BI, Ramming DW, Owens CL, Li L, Buckler ES, Cadle-Davidson L (2015) Genetic mapping in grapevine using SNP microarray intensity values. Molecular Breeding (2015) Molecular Breeding 35:88.
myles_mol_breeding_Rscript.zip – R script and associated files
Python script to parse Genotyping-By-Sequencing data
The following link provides the Python code used to perform quality trimming and barcode deconvolution using Genotyping-By-Sequencing (GBS) data. The files are referred to in the following manuscript: Gardner et al. (in preparation) The genetic structure of the apple.
pythonscript.zip - Python scripts and libraries