Skip to content
A Mathematica pipeline for genetic analysis in multiparental populations
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
RABBIT_Example Scripts
RABBIT_Manual
RABBIT_Packages
RABBIT_Tutorial
.gitattributes
.gitignore
LICENSE
README.md

README.md

RABBIT

RABBIT was developped for Reconstrucing Ancestral Blocks BIT by bit in multiparental populations, which has been extended for genotype imputaiton and genetic map construction. Tested in Matheamtica 11.0.

##Getting started

  1. Clone or download.

  2. Create a new mathematica notebook in a work folder, and set path to the folder "RABBIT_Packages".

  3. Needs["MagicReconstruct`"] for haplotype reconstruciton.

    Needs["MagicImpute`"] for genotype imputation

    Needs["MagicMap`"] and myParallelNeeds["MagicMap`"] for genetic map construction

  4. Manual in the folder "RABBIT_Manual", examples in the folder "RABBIT_Example Scripts", and tutorials in the folder "RABBIT_Tutorial"

##References

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2014. A general modeling framework for genome ancestral origins in multi-parental populations. Genetics. 198: 87-101.

Zheng, C. 2015. Modeling X-linked ancestral origins in multiparental populations. G3: Genes | Genomes | Genetics. 5: 777-801.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2015. Reconstruction of genome ancestry blocks in multiparental populations. Genetics. 200: 1073-1087.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2018. Recursive algorithms for modeling genome blocks in a fixed pedigree. G3: Genes | Genomes | Genetics. 8.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2018. Accurate genotype imputation in multiparental populations from low-coverage sequence. Genetics. 210: 71-82.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2018. Construction of genetic linkage maps in multiparental populations. Manuscript.

You can’t perform that action at this time.