Main tool : VADR
Additional tools:
- perl v5.34.0
- infernal v1.1.5
- ncbi-blast+ v2.15.0
- fasta v36.3.8h (the tool, not the file format)
- minimap2 2.26-r1175
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.
Included models:
- HAV version 1.0.0 (
-mkey hav.vadr)
Most of the VADR model files are located at /opt/vadr/vadr-models in the container filesystem and this path is stored in the globally accessible bash variable $VADRMODELDIR. For most applications, there is no need to specify v-annotate.pl --mdir /path/to/model/files since $VADRMODELDIR is set in the environment.
- Full documentation: https://github.com/ncbi/vadr/wiki
- HAV model documentation: https://github.com/theiagen/VADR_models
# trim fasta file
fasta-trim-terminal-ambigs.pl input.consensus.fa > trimmed.fasta
# run v-annotate.pl using HAV models to annotate an HAV FASTA file
# the "-mkey hav.vadr" option is required to specify the HAV model
v-annotate.pl --split \
-r \
-xnocomp \
-mkey hav.vadr \
trimmed.fasta \
hav-test-output
# 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