EbolaSeq is a command-line tool that simplifies the process of analyzing Ebola virus sequences. It automates the complete workflow from downloading sequences to creating phylogenetic trees. The tool retrieves Ebola virus sequences from NCBI GenBank, processes them according to user specifications, performs multiple sequence alignment and generates phylogenetic trees.
First, install conda if you haven’t already:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Then, ensure you have the required channels:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Install Install EbolaSeq via Conda:
conda create -n ebolaseq -c bioconda ebolaseq -y
conda activate ebolaseq
conda create -n ebolaseq -c bioconda python=3.9 mafft trimal iqtree
conda activate ebolaseq
git clone https://github.com/DaanJansen94/ebolaseq.git
cd ebolaseq
pip install .
conda activate ebolaseq # Make sure you're in the right environment
cd ebolaseq
git pull # Get the latest updates from GitHub
pip uninstall ebolaseq
pip install .
Note: Any time you modify the code or pull updates from GitHub, you need to reinstall the package using these commands for the changes to take effect.
First, make sure your conda environment is activated:
conda activate ebolaseq
EbolaSeq can be run in two modes:
Basic command structure:
ebolaseq --output-dir my_analysis [optional arguments]
Example commands:
# Basic usage
ebolaseq --output-dir my_analysis
# With phylogenetic analysis
ebolaseq --output-dir my_analysis --phylogeny
# Complete analysis with sequence removal and consensus
ebolaseq --output-dir my_analysis \
--consensus-file path/to/consensus.fasta \
--remove remove.txt \
--phylogeny
The tool will interactively prompt you for choices about:
For HPC submissions or automated runs, specify all parameters via command line:
ebolaseq --output-dir my_analysis \
--virus 1 \
--genome 2 \
--completeness 80 \
--host 1 \
--metadata 3 \
--beast 2 \
--phylogeny \
--consensus-file path/to/consensus.fasta \
--remove remove.txt
Required parameters for non-interactive mode:
--virus: Virus type
--genome: Genome completeness
--completeness: Required when –genome=2
--host: Host filter
--metadata: Metadata filter
--beast: Required when –metadata is 2 or 3
Optional arguments (both modes):
--output-dir: Output directory (required)--consensus-file: Path to consensus FASTA file--remove: Path to sequence removal list--phylogeny: Create phylogenetic tree>Consensus_sequence_name
ATGCATGCATGC...
KM034562.1
KM034563.1
MK114118.1
It is strongly recommended to always use a remove.txt file with the --remove option when running EbolaSeq. This file should contain sequence IDs that should be excluded from the analysis, particularly sequences obtained from cell culture passages, laboratory-adapted strains, artificially modified sequences, sequences from experimental infections, and other non-natural viral sequences. These sequences can bias analyses as they may not represent natural viral diversity.
When creating large phylogenetic trees for Zaire ebolavirus, it is recommended to root the tree using sequences from the 1976 Yambuku outbreak, as this represents the first documented outbreak of the virus.
If you use EbolaSeq in your research, please cite:
Jansen, D., & Vercauteren, K. (2025). EbolaSeq: A Command-Line Tool for Downloading, Processing, and Analyzing Ebola Virus Sequences for Phylogenetic Analysis (v0.1.1). Zenodo. https://doi.org/10.5281/zenodo.14851686
This project is licensed under the GNU General Public License v3.0 (GPL-3.0) - see the LICENSE file for details.
Contributions are welcome! Please feel free to submit a Pull Request.
If you encounter any problems or have questions, please open an issue on GitHub.