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
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.
This image does not contain any VADR models by default, as the files are large and result in a large/bloated docker image. This is meant to be the "slim" docker image for VADR v1.7 and is useful in bioinformatics workflows (especially those run in the cloud/HPC environments) as the overhead for downloading the docker image is lower than the docker images that do include the models.
VADR models should be downloaded separately and mounted/bound to the container at runtime. 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.
# 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# 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>