Reneo: Unraveling Viral Genomes from Metagenomes

Reneo means to unravel or untangle in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both prokaryotic and eukaryotic viruses) found within metagenomes using assembly graphs. Reneo identifies viral components in the metagenomic assembly using virus orthologous groups from VOGDB, models as flow networks and solves a minimum flow decomposition (MFD) problem to resolve genomic paths. Reneo was motivated based on a bacteriophage recovery tool named Phables, specifically to extend the capabilities of Phables to all viruses.

NEW: Reneo is available on Bioconda at https://anaconda.org/bioconda/reneo and on PyPI at https://pypi.org/project/reneo.

Setting up Reneo

Option 1: Installing Reneo using conda (recommended)

You can install Reneo from bioconda at https://anaconda.org/bioconda/reneo. Make sure you have conda installed.

# create conda environment and install reneo
conda create -n reneo -c conda-forge -c anaconda -c bioconda reneo

# activate environment
conda activate reneo

Now you can go to Setting up Gurobi to configure Gurobi.

Option 2: Installing Reneo using pip

You can install Reneo from PyPI at https://pypi.org/project/phables/. Make sure you have pip and mamba installed.

pip install reneo

Now you can go to Setting up Gurobi to configure Gurobi.

Setting up Gurobi

The MFD implementation uses the linear programming solver Gurobi. The reneo conda environment does not include Gurobi. You have to install Gurobi using the following command.

conda install -c gurobi gurobi

To handle large models without any model size limitations, once you have installed Gurobi, you have to activate the (academic) license and add the key using the following command. You only have to do this once.

grbgetkey <KEY>

You can refer to further instructions at https://www.gurobi.com/academia/academic-program-and-licenses/.

Quick Start Guide

Setting up databases

Run the following command to download and set up the databases used in Reneo.

reneo install

Testing the setup

After setting up, run the following command to print out the Reneo help message.

reneo --help

You can simulate a Reneo run using the following command.

reneo simulate

You can also run Reneo with the test dataset provided.

reneo test

Running Reneo

# Run Reneo
# locally: using 16 threads (default is 8 threads)
reneo run --input assembly_graph.gfa --reads fastq/ --threads 16

Issues and Questions

Reneo is still under testing. Please report any issues and suggestions under Reneo Issues.

Acknowledgement

Reneo uses the Gurobi implementation of MFD-ILP and code snippets from Phables. The Reneo logo was designed by Laura Inglis.

Citation

Reneo is a work in progress and the manuscript is currently in preparation. In the meantime, please cite Reneo as

V Mallawaarachchi, MJ Roach, LK Inglis and RA Edwards (2023). Reneo: Unraveling Viral Genomes from Metagenomes. Available at https://github.com/Vini2/reneo DOI: 10.5281/zenodo.8263066