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:
- MeV/Measles version 1.02 (
-mkey mev)
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/NLM-DIR/vadr/wiki
- MeV documentation: https://github.com/greninger-lab/vadr-models-mev
Please note that VADR may need a large amount of RAM (>16 GB) for many MeV sequences, especially those that are highly divergent.
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
# trim fasta file
fasta-trim-terminal-ambigs.pl input.consensus.fa > trimmed.fasta
# run v-annotate.pl using RSV models
v-annotate.pl --split
-r \
-xnocomp \
-mkey mev \
trimmed.fasta \
mev-test-output