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

Sequences already evaluated with VADR To date, VADR has been used to evaluate hundreds of norovirus and dengue virus sequences submitted to GenBank. During intermediate phases of testing, we recorded in detail the fate of every submitted sequence into six categories. Among 922 norovirus sequences submitted in 2019 during this phase, 898 (97%) were accepted automatically, 8 were accepted by an indexer without changes, 8 were accepted by an indexer after making changes, and 8 were sent back to the submitter. Among 2644 dengue virus sequences submitted from the beginning of 2019 until intermediate testing stopped on February 14, 2020, 2520 (95%) were accepted automatically, 15 were accepted by an indexer without changes, 96 were accepted by an indexer after making changes, 9 were sent back to the submitter, and 4 had a more complicated fate. After VADR was put into full production usage for norovirus, the record-keeping was reduced to record only how many sequences are evaluated by VADR and how many sequences pass or fail. Among the first 3143 norovirus sequences evaluated by VADR in production mode, 2809 (89%) passed while 334 (11%) failed. If these data are representative of norovirus and dengue virus submissions, the expected reduction in the number of sequences that need to be manually reviewed by NCBI indexers (which prior to development of VADR was 100%) will be about 10-fold for norovirus submissions and about 20-fold for dengue virus submissions.