VADR - Viral Annotation DefineR <a name="top"></a>

Version 1.7; September 2025

https://github.com/ncbi/vadr.git

VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It includes models that can be used to validate and annotate Norovirus, Dengue virus, SARS-CoV-2 virus as well as other flaviviruses, caliciviruses, and coronaviruses, plus influenza virus, mpox virus, and respiratory syncitial virus (RSV). Additional models are available to download or can be created using the v-build.pl program.

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Quick-start: install VADR and classify and annotate viral sequences using v-scan.pl<a name="quickstart"></a>

Install VADR:

Download this file:

https://raw.githubusercontent.com/ncbi/vadr/master/vadr-install.sh

possibly with a command like:

curl -o vadr-install.sh https://raw.githubusercontent.com/ncbi/vadr/master/vadr-install.sh

And execute it, with one of the following commands depending on your system type:

sh ./vadr-install.sh linux

OR

sh ./vadr-install.sh macosx-silicon

OR

sh ./vadr-install.sh macosx-intel

Then follow the instructions output at the end of the installation for updating your .bashrc or .cshrc file and defining important environment variables that VADR relies on.

Run v-scan.pl to annotate viral sequences

Given a fasta sequence file called my.fa with any combination of flavivirus, calicivirus, coronavirus, influenza, RSV, or Mpox sequences, run:

v-scan.pl -m in.fa out

This will list each stage of the processing and ultimately create an output directory called out and fill it with output files. Short descriptions of the output files will be printed to the screen. More detailed explanation of output file types can be found here. For a more detailed walk-through example of v-scan.pl see this page.

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VADR programs

The VADR v-scan.pl script classifies and annotates sequences that match to any of your VADR model libraries. Once v-scan.pl determines the library to use for a given set of sequences, it runs a different VADR program called v-annotate.pl which identifies the appropriate model in the library to use for each sequence and defines the annotation based on that most similar model. v-scan.pl will automatically run v-annotate.pl using the recommended settings (v-annotate.pl command-line options) for each library but alternatively, users can run the v-annotate.pl separately. Example usage of v-annotate.pl can be found here.

Another VADR script, v-build.pl, is used to create the models from individual sequences from GenBank or from input multiple sequence alignments, potentially with secondary structure annotation. v-build.pl stores the GenBank feature annotation in the model, and v-annotate.pl maps that annotation (e.g. CDS coordinates) onto the sequences it annotates. Example usage of v-build.pl can be found here. An advanced tutorial on building VADR models using RSV as an example can be found here.

v-annotate.pl identifies unexpected or divergent attributes of the sequences it annotates (e.g. invalid or early stop codons in CDS features) and reports them to the user in the form of alerts. A subset of alerts are fatal and cause a sequence to fail. A sequence passes if zero fatal alerts are reported for it. VADR is used by GenBank staff to evaluate incoming sequence submissions of some viruses (currently Norovirus, Dengue virus, and SARS-CoV-2). Submitted Norovirus, Dengue virus and SARS-CoV-2 sequences that pass v-annotate.pl are accepted into GenBank.

The homology search and alignment components of VADR scripts, the most computationally expensive steps, are performed by the Infernal, HMMER, FASTA, MINIMAP2 and BLAST software packages, which are downloaded and installed with VADR installation.

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VADR model libraries <a name="models"></a>

VADR installation includes the following model libraries:

| library | model key (short name) | rigorously tested? | number of models | notes | |--------------|------------------------|--------------------|------------------|-------| | Caliciviridae | calici | norovirus models only | 49 | norovirus models used by GenBank | | Flaviviridae | flavi | dengue and HCV models only | 156 | dengue models used by GenBank | | Coronaviridae | corona | SARS-CoV-2 only | 55 | SARS-CoV-2 models used by GenBank | | influenza | flu | yes | 70 | described in Database article | | Mpox | mpxv | yes | 1 | | | respiratory syncitial virus (RSV) | rsv | yes | 2 | |

Additional models are available. See this page for a list of all available models and additional information.

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VADR documentation <a name="documentation"></a>

• VADR installation instructions
  • Installation using vadr-install.sh
  • Setting environment variables
  • Verifying successful installation
  • Further information
• v-build.pl example usage and command-line options
  • v-build.pl example usage
  • v-build.pl command-line options
  • Building a VADR model library
  • How the VADR 1.0 model library was constructed
• v-annotate.pl example usage, command-line options and alert information
  • v-annotate.pl example usage
  • Running v-annotate.pl inside the v-scan.pl wrapper
  • v-annotate.pl command-line options
  • Basic Information on v-annotate.pl alerts
  • Additional information on v-annotate.pl alerts
• v-scan.pl example usage and command-line options
  • Quickstart v-scan.pl examples
  • The v-scan.pl config file
  • Walk-throughs of v-scan.pl examples
  • v-scan.pl command-line options
• Advanced tutorial: building an RSV model library
• Explanations and examples of v-annotate.pl detailed alert and error messages
  • Output fields with detailed alert and error messages
  • Explanation of sequence and model coordinate fields in .alt files
  • toy50 toy model used in examples of alert messages
  • Examples of different alert types and corresponding .alt output
  • Posterior probability annotation in VADR output Stockholm alignments
• VADR output file formats
  • VADR output files created by all VADR scripts
  • v-build.pl output files
  • v-annotate.pl output files
  • VADR coords coordinate string format
  • VADR sequence naming conventions
• Available VADR model files (github wiki)
• SARS-CoV-2 annotation (github wiki)
• Rfam-based structural annotation of a viral genome sequence for use with VADR (github wiki)
• Development notes and instructions (github wiki)

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Contributors <a name="contributors"></a>

• VADR includes contributions and input from current and former colleagues at NCBI, including:

  Rodney Brister

  Vince Calhoun

  Sergiy Gotvyanskyy

  Eneida Hatcher

  Sophia Hu

  Ilene Karsch-Mizrachi

  Rich McVeigh

  Susan Schafer

  Alejandro Schäffer

  Lara Shonkwiler

  Beverly Underwood

  Yuri Wolf

  Linda Yankie

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Reference <a name="reference"></a>

• The recommended citation for influenza analysis using VADR is: Vincent C Calhoun, Eneida L Hatcher, Linda Yankie, Eric P Nawrocki; Influenza sequence validation and annotation using VADR. Database. baae091. (2024). https://doi.org/10.1093/database/baae091

• The recommended citation for using VADR for SARS-CoV-2 analysis: Eric P Nawrocki; Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR. NAR Genom Bioinform. 2023 Jan 20;5(1)::lqad002. (2023). https://doi.org/10.1093/nargab/lqad002

• The recommended citation for all other uses of VADR is: Alejandro A Schäffer, Eneida L Hatcher, Linda Yankie, Lara Shonkwiler, J Rodney Brister, Ilene Karsch-Mizrachi, Eric P Nawrocki; VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics 21, 211 (2020). https://doi.org/10.1186/s12859-020-3537-3

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Questions, comments or feature requests? Send a mail to eric.nawrocki@nih.gov.