Author: Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki
Title: VADR: validation and annotation of virus sequence submissions to GenBank Document date: 2019_11_22
ID: besvz92f_63
Snippet: Based on this analysis for the NC results, VADR had a false positive rate of 0 and a false negative rate of 0.12 (18/147). Both VAPiD and VIGOR had a false positive rate of 0.33 (1/3) and a false negative rate of 0. Because one of the design goals of VADR is to prevent problematic sequences from automatic deposition into GenBank, it is more important to minimize the FP rate than the FN rate. While VADR's FN rate is considerably higher than that o.....
Document: Based on this analysis for the NC results, VADR had a false positive rate of 0 and a false negative rate of 0.12 (18/147). Both VAPiD and VIGOR had a false positive rate of 0.33 (1/3) and a false negative rate of 0. Because one of the design goals of VADR is to prevent problematic sequences from automatic deposition into GenBank, it is more important to minimize the FP rate than the FN rate. While VADR's FN rate is considerably higher than that of VIGOR and VA-PiD, the 18 FN sequences that fail VADR all deviate from the nearest RefSeq in specific ways such that Gen-Bank indexers want to manually examine them. Later, we calculate FP and FN rates for new norovirus and dengue submissions evaluated with VADR which show that the FN rate can be significantly lower in practice.
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