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

For bacterial genomes, these limitations have been addressed by the release of NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) [6] , which is now available for download as a standalone package (https://github.com/ncbi/pgap/releases). For influenza virus, the limitations were addressed first by FLAN [2] and then by the influenza virus submission tools provided by GenBank [3] . Tools for checking submissions of non-influenza viruses have lagged but in the work described herein we describe new software that begins to close the gap. Importantly, our new software can already be used for many viruses (currently excluding circular genome and segmented viruses) breaking from the paradigm of developing code for one virus at a time that has limited the breadth of the Virus Variation Resource.