Read, Standardize and Translate Genomic Data • genometranslator

genometranslator reads, standardizes, and writes individual genomic data. The easiest interface is read_genome and write_genome; use a format-specific read_* or write_* function when more control is needed.

Installation

genometranslator uses CRAN, Bioconductor, and GitHub dependencies. Starting from a basic R installation, install the required dependencies with:

install.packages(c("BiocManager", "remotes"))

BiocManager::install(c(
  "gdsfmt",
  "Rsamtools",
  "SeqArray"
))

remotes::install_github("thierrygosselin/tgbase")
remotes::install_github("thierrygosselin/genometranslator")

Optional R packages

Install only the packages needed by your workflow:

# Interested in genind and/or genlight requires: 
install.packages("adegenet")

See the documentation for the relevant read_* or write_* function for the exact dependency and data requirements of that format.

Run the dependency diagnostic after installation:

genometranslator::genometranslator_dependencies()

Optional bcftools executable

Some VCF preparation and indexing operations use bcftools. It is not an R package and cannot be installed with install.packages().

If Conda is not already available, install Miniforge, restart the terminal, and confirm that Conda is working:

conda --version

Create the shared genomics environment when it does not already exist:

conda create --name genomics --channel conda-forge --channel bioconda bcftools

For an existing genomics environment, install or update bcftools with:

conda activate genomics
conda install --channel conda-forge --channel bioconda bcftools

Confirm the installation before starting R or RStudio:

conda activate genomics
bcftools --version
which bcftools

Start R or RStudio from the activated environment. Inside R, verify that the executable is visible:

Sys.which("bcftools")
genometranslator::genometranslator_dependencies()

An empty result from Sys.which("bcftools") means that the current R session cannot see the Conda environment. Close R/RStudio, activate genomics, and start it again from that terminal session.

Citation

To obtain the canonical citation for the installed package version, use:

citation("genometranslator")

When reporting an analysis, include at least the package version:

packageVersion("genometranslator")

For a development version, reproducibility is improved by also recording the Git commit used. The access date is useful additional context, especially while the package is under active development, but it should not replace the version or commit identifier.

A citation can be described in this form until a dedicated publication or DOI is available:

Gosselin, T. (2026). genometranslator: Read, standardize and translate genomic data. R package version 0.0.0.9000. https://github.com/thierrygosselin/genometranslator. Accessed 2026-08-23.

Website and support

Documentation and articles are available at https://thierrygosselin.github.io/genometranslator/.

Report problems or request features through the GitHub issue tracker.