Reads2Map Tools

Contains utilities functions for Reads2Map workflows usage:

Uses as inputs VCF files to run updog, polyRAD and SuperMASSA and converts the output to onemap object or VCF files;
Simulates mapping populations using PedigreeSim software and converts the output to onemap object or VCF files;
Draws samples haplotypes from phased VCF files.

How to install

install.packages("devtools")
devtools::install_github("Cristianetaniguti/Reads2MapTools")

This package is one of the tools used in Reads2Map workflows. You can find it in the docker image cristaniguti/reads2map. Usage through docker:

docker pull cristaniguti/reads2map:0.0.2

Documentation

Check features description and example of usage here.

You can also find more details about the simulations and how they can be applied in:

Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092