VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki

VADR model library VADR includes a library of models generated by vbuild.pl, represented by a "vadr.minfo" model info file, a "vadr.cm" CM file, and BLAST database files that include information and models for 194 viral RefSeq genomes (v1.0 VADR library). These 194 RefSeqs comprise 9 norovirus sequences, 4 dengue virus sequences, and an additional 181 RefSeqs from other viruses in the families Caliciviridae and Flaviviridae. The additional 181 RefSeqs allow VADR to recognize when an input sequence purported to be norovirus or dengue virus is in fact a different Caliciviridae or Flaviviridae taxon. This library is currently used by GenBank indexers on submitted sequences to annotate norovirus and dengue virus sequences and to recognize some taxonomically misclassified sequences. Users are able to build their own model libraries with v-build.pl to use instead of this default library. We plan to add additional models to the default set in future versions after testing them internally at NCBI.