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

Limitations and future directions One obvious limitation of VADR at present is that it is used at NCBI only for norovirus and dengue virus sequences, but not yet for other viruses. Near-term plans include to expand the usage to many other members of the family Flaviviridae, including Hepacivirus C, West Nile virus and Zika virus. VADR was not designed for viruses with genomes larger than 25Kb such as eukaryotic DNA viruses such as Epstein-Barr virus (∼170Kb). For these larger viruses, VADR would require an impractical amount of memory and time due to the high complexity of the CM algorithms. In future work, we hope to develop new methods to alleviate this restriction. Due to the COVID-19 outbreak beginning in December 2019, we have made 55 Coronaviridae models available for download and analysis of coronavirus sequences including SARS-CoV-2, even though VADR was not designed for sequences as large as coronavirus genomes (∼30Kb). It is recommended that at least 64Gb of RAM are available when analyzing full length coronavirus genomes. Download and usage instructions for these models can be found on github (https://github.com/nawrockie/vadr/wiki/Available-VADR-model-files).