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 either the --mdir and --mkey options to v-annotate.pl as shown in the SARS-CoV-2 example here, or with some combination of the -m, -a, -i, -n, and -x options. Those options are described more here

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SARS-CoV-2 and other Coronaviridae RefSeq VADR models

• FTP page with current model file gzipped tarball
• 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.

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Norovirus and Dengue virus and other Flaviviridae and Caliciviridae RefSeq VADR models

• THIS SET OF MODELS IS INSTALLED WITH VADR and is referred to in the documentation as the "default" set of models
• FTP page with current model file gzipped tarball
• 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

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Metazoan Cytochrome c oxidase I (COX1) VADR models

• FTP page with current model file gzipped tarball
• see the 00README.txt file included in the tarball of models for more information and recommended v-annotate.pl commands.
• 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.

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