Available VADR model files

You can download pre-built models to use to validate and annotate viruses or cox1 genes as listed below. Importantly, to use a set of models other than the default set that is installed with VADR, you will need to use use the -m, -i and -b options as described here.

• VADR models for Norovirus and Dengue virus RefSeqs along with other Flaviviridae and Caliciviridae RefSeqs.

  • THIS SET OF MODELS IS INSTALLED WITH VADR and is referred to in the documentation as the "default" set of models
  • this link will download the specific set of models (vadr-models-1.0-1.tar.gz) used in the manuscript describing VADR v1.0
  • construction of this set of models is detailed here

• VADR models for Coronaviridae RefSeqs, including 2019-nCoV (NC_045512)

  • see the 00README.txt file included in the tarball of models for more information and recommended v-annotate.pl commands.

  • WARNING: using v-annotate.pl with these models requires a lot of RAM (64Gb recommended) and you will need to add the option --mxsize 64000 to your v-annotate.pl commands.

  • these models (~30Kb) are larger than the maximum length (25Kb) allowed by v-build.pl and were built with a still in-development version of VADR that is not yet publicly available.

• VADR models for metazoan Cytochrome c oxidase I (COX1)

  • these models are currently in testing for analyzing metazoan cox1 sequence submissions to GenBank
  • these models were built from alignments instead of single RefSeqs, email [email protected] if you want the alignments