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Available VADR model files

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Eric Nawrocki edited this page Apr 9, 2021 · 33 revisions

You can download pre-built models to use to validate and annotate virus sequences or cox1 gene sequences 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 either the --mdir and --mkey options to v-annotate.pl as shown in the SARS-CoV-2 example on this page, or with some combination of the -m, -a, -i, -n, and -x options. Those options are described more here.

##SARS-CoV-2 and other Coronaviridae RefSeq VADR models

##Norovirus and other Caliciviridae RefSeq VADR models

  • THIS SET OF MODELS IS INSTALLED WITH VADR (current set is installed with VADR v1.2) and is referred to in the documentation as the "default" set of models

  • these models are currently used to validate and annotate incoming Norovirus sequence submissions to GenBank using the following options:

    v-annotate.pl --group Norovirus --nomisc --noprotid <fasta-file-to-annotate> <output-directory-to-create>

  • Previously (v 1.1.3 and earlier) the default set of models included both Caliciviridae and Flaviviridae models, but as of v1.2 they are split into two model sets, although both are installed by the VADR installation script.

  • FTP page with current model file gzipped tarball

  • Bitbucket repo for these models (includes set 1.2-1 (March 2021) and later)

  • this link will download the specific set of models (vadr-models-1.0-1.tar.gz) used in the manuscript describing VADR v1.0. The construction of the v1.0 set of models is detailed here

##Dengue virus and other Flaviviridae RefSeq VADR models

  • THIS SET OF MODELS IS INSTALLED WITH VADR (current set is installed with VADR v1.2) to in the documentation as the "default" set of models

  • these models are currently used to validate and annotate incoming Dengue virus sequence submissions to GenBank using the following options:

    v-annotate.pl --group Dengue --nomisc --noprotid --mkey flavi <fasta-file-to-annotate> <output-directory-to-create>

  • Previously (v 1.1.3 and earlier) the default set of models included both Caliciviridae and Flaviviridae models, but as of v1.2 they are split into two model sets, although both are installed by the VADR installation script. To use the Flaviviridae model set, you'll need to use the --mkey flavi option with v-annotate.pl.

  • FTP page with current model file gzipped tarball

  • Bitbucket repo for these models (includes set 1.2-1 (March 2021) and later)

##Metazoan Cytochrome c oxidase I (COX1) VADR models

  • FTP page with current model file gzipped tarball

  • these models are currently used to validate and annotate incoming Norovirus sequence submissions to GenBank using the following options:

    v-annotate.pl --xmaxdel 3 --xmaxins 3 --xlongest --mkey cox1 --alt_pass lowcovrg --alt_fail fsthicnf,fstlocnf --fstlowthr 0.0 --fstminnt 5 --nomisc --noprotid --xsub <cox1-models-dir-path>/cox1.phy.xsub --mdir <cox1-models-dir-path> <fasta-file-to-annotate> <output-directory-to-create>

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

  • Bitbucket repo for these models (includes set 1.2-1 (March 2021) and later)

  • these models are currently in testing for analyzing metazoan cox1 sequence submissions to GenBank

  • these models were built from alignments instead of single RefSeqs. The alignments are included in Stockholm format in the tarballs as .stk files.

Questions, comments, feature or model requests? Send a mail to [email protected].

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