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Theiagen Genomics VADR Models

VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families.

VADR works with two main scripts: v-build.pl stores the RefSeq feature annotation in the model, and v-annotate.pl maps that annotation (e.g. CDS coordinates) onto the sequences it annotates. VADR's v-build.pl is used to create VADR models from NCBI RefSeq sequences, potentially with secondary structure annotation.

Custom VADR Models

HAV

The custom HAV VADR model was constructed with RefSeq sequence NC_001489. The command used was the following

v-build.pl -f --group HAV --subgroup IA NC_001489 hav

VADR, version 1.6.3, was executed with the container us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.3

Further details:

  • reference sequence assembly: NC_001489
  • version number of assembly: 1
  • source of assembly: RefSeq
  • URL where assembly was downloaded: https://www.ncbi.nlm.nih.gov/nuccore/NC_001489.1
  • date of access and download of assembly: February 6th, 2024
  • details of any modifications made to assembly: None performed

Contact

For any inquiries please contact us at [email protected].