Reads2Map Tools

Aug 1, 2023 · 1 min read

Reads2Map Tools bundles the R utilities behind the Reads2Map workflows described in Taniguti et al. (2023, GigaScience 12). It automates genotype calling, population simulation, and file conversions so users can build end-to-end pipelines for linkage-map construction.

What it does

  • Uses VCF inputs to run updog, polyRAD, and SuperMASSA, and converts their outputs to onemap objects or VCF files.
  • Simulates mapping populations via PedigreeSim and exports compatible objects for downstream analysis.
  • Draws sample haplotypes from phased VCFs, easing reproducible marker validation.
  • Ships inside the cristaniguti/reads2map Docker image so the full workflow is container-ready.

Package details

  • Version 0.3.4 (development); install via devtools::install_github("Cristianetaniguti/Reads2MapTools").
  • Depends on R ≥ 4.0 and imports doParallel, matrixStats, updog, polyRAD, dplyr, ggplot2, ggpubr, lubridate, onemap, stringr, tidyr, vcfR, gtools.
  • Maintainer: Cristiane Taniguti chtaniguti@usp.br; contributors include colleagues from the GigaScience Reads2Map paper.
  • License: GPL-3.

The package underpins the Reads2Map workflows and accompanying Docker images, enabling reproducible GBS analyses for linkage-map projects.

R Package Genotyping-by-Sequencing Linkage Maps Workflows
Thiago de Paula Oliveira
Authors
Thiago de Paula Oliveira
Statistician | Data Quality | Statistical Computing