VIPER is a user-friendly toolkit for assembling and identifying viral genomes (SARS-CoV-2, Dengue, and Influenza) from Illumina sequencing data. Created by the CeVIVAS bioinformatics team at the Butantan Institute, VIPER combines an intuitive Windows GUI with robust command-line pipelines.
- Multi-virus pipelines with curated references and lineage assignment.
- Windows GUI for non-technical users; Linux command-line for servers and pipelines.
- Resource-aware execution: tested in low computational resources setups.
- Open source and customizable for lab or surveillance workflows.
- SARS-CoV-2 assembly (Illumina)
- Dengue assembly (Illumina)
- Influenza assembly (Illumina)
- Download the Windows installer (
.exe) from the project Releases. The installer bundles the GUI and sets up the WSL-based backend. - Requirements: Windows 10 2004+ (build 19041+) or Windows 11, admin permissions, and ~10 GB free disk space. An internet connection is required to download dependencies during setup.
- Antivirus tools can flag installers; if that happens, whitelist the VIPER installer.
Step-by-step with screenshots
- Choose optional tasks (desktop shortcut).
- Confirm installation.
- Copying files.
- Core/WSL bootstrap.
- Allow WSL enablement/restart if prompted.
- Windows enabling WSL.
- Bootstrap inside WSL (micromamba + environment).
- Packages being installed.
- Finalizing links and PATH inside WSL.
- Finish the installer.
After installation, launch VIPER from the Start menu or run VIPER.exe from the installation folder. If you need to uninstall, use Windows Apps & Features and, if requested, run wsl --unregister VIPER-Core from an elevated PowerShell.
On Linux, VIPER runs via command line only.
Prerequisites
- Bash, git, curl, and
sudo(for optional symlinks). - Micromamba or Conda (micromamba recommended).
- Python 3.8 (handled by the environment YAML).
1) Get the code
git clone https://github.com/V-GEN-Lab/viper.git
cd viper2) Install micromamba (if you do not already have micromamba/conda)
Example for bash:
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
./bin/micromamba shell init -s bash -p ~/.local/share/micromamba
source ~/.bashrc3) Create the VIPER environment
The YAML pins all dependencies. It sets the prefix to ~/.local/share/mamba/envs/VIPERGenomeAssembler.
micromamba create -y -f Pipelines/VIPERGenomeAssemblerLinux.yaml
micromamba activate VIPERGenomeAssembler
# If activation by name does not work in your shell session, initialize your shell first:
# micromamba shell init -s bash -p ~/.local/share/micromamba
# source ~/.bashrc
# micromamba activate VIPERGenomeAssembler4) Make the pipeline scripts available
Option A (recommended, creates /usr/local/bin/VIPER_*.sh wrappers):
sudo bash update.d/post-update.shOption B (no sudo): add the modules folder to PATH and expose $PIPELINE:
export PIPELINE="$(pwd)/Pipelines/Modules"
echo 'export PIPELINE="$HOME/viper/Pipelines/Modules"' >> ~/.bashrc
echo 'export PATH="$PIPELINE:$PATH"' >> ~/.bashrc
source ~/.bashrc
# If your repository is not in $HOME/viper, replace that path accordingly.
# configurePATH.sh may not work in every restricted or non-sudo environment, so manually exporting PIPELINE and updating PATH is the safest approach for shared servers.Launch VIPER.exe. The GUI has a basic and an advanced view:
In the Advanced tab, you can change the maximum RAM VIPER may use: enter the value in the required format, click Apply, then use Update to confirm it applied.
VIPER refreshes viral databases before running; you can also trigger database updates manually when needed.
Choose how many threads VIPER will use for assembly before starting a run.
Run pipeline steps:
- Select the folder containing your
*.fastq.gzpairs.
1.1) Choose the viral pipeline.
- After selecting folder and pipeline, review the summary and continue.
- Pipeline executed successfully; confirmation message displayed.
- Choose whether to open a simplified dashboard to view results.
- Dashboard view; export results to Excel if needed.
- Generated outputs in the pipeline folder (.fasta genomes plus per-sample subfolders with additional files).
Manual database update (optional):
Activate the environment first:
micromamba activate VIPERGenomeAssemblerIf you ran update.d/post-update.sh, use the wrappers:
# {threads} = threads per sample, {samples} = parallel samples
VIPER_CoV.sh {threads} {samples} # SARS-CoV-2
VIPER_DENV.sh {threads} {samples} # Dengue
VIPER_FLU.sh {threads} {samples} # InfluenzaIf you used configurePATH.sh without sudo, run directly via $PIPELINE:
bash "$PIPELINE/SARS-CoV-2/Exec_assembly_pipeline_Illumina_v8_bowtie2_ref_iVar_CeVIVAS.sh" {threads} {samples}
bash "$PIPELINE/DENV/Exec_assembly_pipeline_Illumina_v5_bwa_mem_ref_iVar.sh" {threads} {samples}
bash "$PIPELINE/Influenza/Exec_assembly_pipeline_Illumina_v3_Vapor_SPAdes.sh" {threads} {samples}Results are written next to the input FASTQ directory. Test datasets are available under Test_samples/.
SARS-CoV-2 assembly overview
Dengue assembly overview
Influenza assembly overview
- Pipelines for additional viruses (e.g., Chikungunya, RSV).
- Automatic detection of the virus type being analyzed.
- Phylogeny module with interactive tree visualization via Auspice.
- Reworked assembly modules for iSNV detection.
- Allow users to supply custom reference sequences for assembly.
- Pipeline optimization for workflow managers (e.g., Snakemake, Nextflow).
VIPER was created by the CeVIVAS bioinformatics team at the Butantan Institute:
- Alex Ranieri J. Lima
- Gabriela Ribeiro
- Vinicius Carius De Souza
- Isabela Carvalho Brcko
- Igor Santana Ribeiro
- James Siqueira Pereira
- Vincent Louis Viala
Supervised by:
- Maria Carolina Quartim Barbosa Elias Sabbaga
- Sandra Coccuzzo Sampaio
VIPER is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
VIPER is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details: http://www.gnu.org/licenses/.