1.7

VADR container

Main tool : VADR

Additional tools:

• perl v5.34.0
• infernal v1.1.5
• ncbi-blast+ v2.17.0
• fasta v36.3.8h (the tool, not the file format)
• minimap2 2.30-r1287

Basic information on how to use this tool:

• executable: v-annotate.pl
• additional executable: fasta-trim-terminal-ambigs.pl
• help: -h
• version: -v

Description

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 has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.

Additional information

⚠️ This docker image DOES contain VADR models by default. We originally intended for this to the the slim docker image, but a change in v1.7's installation script resulted in the models being included in the image. We have left the models in the image for now and have created a separate docker image staphb/vadr:1.7-slim which does not include the models. Please see the dockerfile & README here for the actual "slim" version of the vadr docker image: build-files/vadr/1.7-slim/.

These model files are included:

• Coronaviridae (coronaviruses including sars-cov-2) v1.3-3
• Influenza v1.6.3-2
• MPXV v1.4.2-1
• RSV v1.5-2
• SARS-CoV-2 v1.3-2

The default location for VADR models is /opt/vadr/vadr-models/.

A larger list of vadr models can be found in VADR's documentation for download and mounting/binding during runtime. An example for SARS-CoV-2 is below.

Example Usage

# trim fasta file
fasta-trim-terminal-ambigs.pl input.consensus.fa > trimmed.fasta

# run v-annotate.pl using Flaviviridae model to annotate a Dengue viral genome
v-annotate.pl --split --cpu 1 --group Dengue --nomisc --noprotid \
    --mdir /opt/vadr/vadr-models-flavi/ --mkey flavi \
    trimmed.fasta \
    dengue-test-outdir

# run v-annotate.pl using Caliciviridae model to annotate a Norovirus viral genome
v-annotate.pl \
    trimmed.fasta \
    noro-test-outdir

Downloading a model

# this image doesn't contain any external models
# this examples downloads the SARS-CoV-2 model
wget https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/sarscov2/1.3-2/vadr-models-sarscov2-1.3-2.tar.gz
tar -xf vadr-models-sarscov2-1.3-2.tar.gz

# then mount this directory to VADRMODELDIR when running
# example with docker
docker run <user docker flags> -v vadr-models-sarscov2-1.3-2:/opt/vadr/vadr-models staphb/vadr:latest <vadr command>