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

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/852657 doi: bioRxiv preprint and > 10, 371nt for norovirus and dengue virus, respectively because almost all sequences labeled "complete genome" exceed these lengths. However, there were 5 norovirus and 27 dengue virus sequences shorter than these threshold lengths returned by the above Entrez queries that are annotated "complete genome". Therefore, we revised the queries partitioning each sets of lengths into two disjoint intervals by using the "[slen]" attribute. We refer to the four datasets or selected subsets thereof as "NP", "NC", "DP", and "DC" for Norovirus-Partial, Norovirus-Complete, Dengue-Partial and Dengue-Complete. 32, 190 and 20,973 sequences respectively. Queries 2 and 4 retrieved lists of 1384 and 4580 sequences respectively. The partial sequences far outnumber the complete sequences for these two taxa. For this reason, we avoided design decisions in VADR that would rely on any specific part of the genome being present.