Main tool : VADR
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.
You can find additional information on the SARS-CoV-2 models used by VADR here. The models are downloaded from the NCBI FTP server
Additional tools:
- perl v5.22.1
- infernal v1.1.4
- hmmer v3.3.2
- ncbi-blast+ v2.12.0
- fasta v36.3.8h (the tool, not the file format)
Available VADR models:
- sarscov2 v1.3-2
- mpxv (MonkeyPox) v1.4.2-1
- Norovirus and other Caliciviridae
- Dengue virus and other Flaviviridae
Full documentation: https://github.com/ncbi/vadr#vadr-documentation-
Docs on Coronavirus annotation: https://github.com/ncbi/vadr/wiki/Coronavirus-annotation
Docs on MPXV annotation: https://github.com/ncbi/vadr/wiki/Monkeypox-virus-annotation
Note: Support for MonkeyPox genome annotation was just added in the VADR software (July 2022) and is under active development. Things may change quickly. See the above documentation ^ to see the latest information on the state of MPXV annotation with VADR.
Also be aware that some 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.
# trim terminal Ns from my input genome (VADR requires this as the first step)
# for MPXV, adjust maxlen to 210000
/opt/vadr/vadr/miniscripts/fasta-trim-terminal-ambigs.pl \
/data/SRR13957123.consensus.fa \
--minlen 50 \
--maxlen 30000 \
> /data/SRR13957123.consensus.trimmed.fasta
# run v-annotate.pl using the sarscov2 model to annotate a trimmed input genome
v-annotate.pl --noseqnamemax --glsearch -s -r --nomisc \
--mkey sarscov2 --lowsim5seq 6 \
--lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn \
/data/SRR13957123.consensus.trimmed.fasta \
SRR13957123-vadr-outdir
# run v-annotate.pl using mpxv model to annotate a trimmed input genome
v-annotate.pl --split --cpu 8 --glsearch -s -r --nomisc --mkey mpxv \
--r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin \
mpxv.consensus.trimmed.fasta \
mpxv-vadr-1.4.2-test-output