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:
- MPOX/mpxv version 1.4.2-1 (
-mkey mpxv)
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.
Be aware that some Mpox sequences may take up to 30 minutes to annotate, depending on how divergent it is from the RefSeq NC_063383 sequence. Some sequences may only take a minute or so.
- Full documentation: https://github.com/ncbi/vadr/wiki
- MPOX/MPXV model documentation: https://github.com/ncbi/vadr/wiki/Mpox-virus-annotation
# trim terminal Ns from my input genome (VADR requires this as the first step)
# for MPXV, adjust maxlen to 210000
fasta-trim-terminal-ambigs.pl \
input.consensus.fa \
--minlen 50 \
--maxlen 210000 \
> trimmed.fasta
# run v-annotate.pl using mpxv model
v-annotate.pl --split --cpu 8 --glsearch -s -r --nomisc --mkey mpxv \
--r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin \
--minimap2 --s_overhang 150 \
trimmed.fasta \
mpxv-test-output