VIBRANT

Recover mobile genetic element sequences from metagenomes using metabolic HMM-based virome identification and annotation.

Virus codeGitHub menu_bookPaper scheduleApril 3, 2026

Installation

Create a conda environment:

conda create -n vibrant_env python=3.5

Activate the environment:

conda activate vibrant_env

Install the packages needed to run VIBRANT:

conda install -c conda-forge biopython
conda install -c anaconda pandas
conda install matplotlib
conda install seaborn
pip install --upgrade numpy==1.17.0
pip install --upgrade scikit-learn==0.21.3
pip install pickle-mixin

Install VIBRANT:

conda install -c bioconda vibrant

Download the database

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This command only needs to be run once — right after the program is installed.

download-db.sh

Run

Concatenate all nucleotide sequences (.fna) files into one file (Genomes.fna):

cat *.fna >> Genomes.fna

Activate the conda environment containing the program:

conda activate vibrant_env

Run VIBRANT:

VIBRANT_run.py -i Genomes.fna -t 20

Output

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On GitHub and on your computer there is a file called output_explanations.pdf with a more detailed explanation of each output the program generates.

Main files in the VIBRANT output folder:

File	Description
.faa	Prodigal protein prediction
.ffn	Prodigal gene prediction
.log	Summary numbers of what was analysed and found