RepGenR

Introduction

RepGenR (Representative-Genome Repositories) is a bioinformatics tool designed to streamline the process of clustering genome sequences. It uses average nucleotide identity (ANI) to produce representative genome repositories, providing researchers with a more manageable dataset for large-scale genomic studies.

Features

RepGenR offers a suite of features to facilitate the organization and analysis of genomic data:

• Taxa selection from the GTDB (Genome Taxonomy DataBase).
• Downloading and formatting genome sequences into a standardized naming convention.
• De-replication of genomes based on average nucleotide identity (ANI).
• Phylogenetic tree computation for both dereplicated and all sequence datasets.
• Generation of phylogenetic trees in a format compatible with downstream processes such as FlexTaxD.

Getting Started

To begin using RepGenR, please consult the wiki for detailed installation instructions and usage guidelines.

Installation

Quick installation guide for users who are familiar with the command line:

# Create a new environment and install dependencies. Make sure to activate the environment before installing RepGenR.
mamba create -n RepGenR -y python=3 matplotlib requests drep checkm-genome ncbi-datasets-cli mashtree progressivemauve iqtree ete3

# Clone the repository
git clone https://github.com/FOI-Bioinformatics/repgenr.git

# Navigate to the RepGenR directory and install
cd repgenr
pip install .

# For detailed installation instructions please refer to the wiki

Usage

For a complete guide on how to use RepGenR, please refer to the wiki. Here's a quick start command to get you running:

# Replace with actual usage command
repgenr --help

See module wiki page for available sub commands.

Contributing

We welcome contributions to RepGenR! If you have suggestions or contributions, please open an issue or pull request.

License

RepGenR is licensed under the MIT License.