Genotyping Uncertainty with Sequencing data and linkage MAPping (GUSMap).

An R package for performing linkage mapping using low and/or high coverage sequencing data without requiring filtering with respect to read depth.

The easiest way to install GUSMap in R is using the devtools package.

install.packages("devtools")
library(devtools)
install_github("tpbilton/GUSbase")
install_github("tpbilton/GUSMap")

Note: Some of the functions are coded in C and therefore an appropriate C compiler is needed for the package to work. For windows OS, Rtools (https://cran.r-project.org/bin/windows/Rtools/) provides a compiler.

The best way to understand how to sue GUSMap to construct linkage maps is to read through the Introduction Tutorial contained in the package.

There are plans to contiune extending this package. If you have any suggests for improvement or additional features you like to see, I'd suggest posting a question under the Issues. I'm also happy for people to suggest changes via a pull request provided it fits within the favour of the package.

To cite this R package:

Bilton, T.P., Schofield, M.R., Black, M.A., Chagné, D., Wilcox, P.L., & Dodds, K.G. (2018). Accounting for errors in low coverage high-throughput sequencing data when constructing genetic maps using biparental outcrossed populations. Genetics, 209(1), 65--76. doi:10.1534/genetics.117.300627

The initial development of this package was partially funded by the Ministry of Business, Innovation and Employment via its funding of the “Genomics for Production & Security in a Biological Economy” programme (Contract ID C10X1306).