Available VADR model files

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.

SARS-CoV-2 and other Coronaviridae RefSeq VADR models

* 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 Norovirus and Dengue virus

RefSeqs](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/CURRENT)
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](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/CURRENT/vadr-models-1.0-1.tar.gz)
  will download the specific set of models
  (vadr-models-1.0-1.tar.gz) used in the [manuscript describing VADR
  v1.0](https://www.biorxiv.org/content/10.1101/852657v1) 
* construction of this set of models is detailed
  [here](documentation/build.md#1.0library)

VADR models for metazoan Cytochrome c oxidase I (COX1)

* 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 eric.nawrocki@nih.gov.