ArticleNAR genomics and bioinformatics2023
Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed, 7 citations in OpenAlex.
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- VICAST: An Integrated Toolkit for Viral Genome Annotation Curation and Low-Frequency Variant Analysis in Passage Studies.bioRxiv : the preprint server for biology · 2026Article
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Automated annotation and validation of human respiratory virus sequences using VADR.Database : the journal of biological databases and curation · 2025Article
- Influenza sequence validation and annotation using VADR.Database : the journal of biological databases and curation · 2024Article
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
- Influenza sequence validation and annotation using VADR.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Update of
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In 2020 and 2021, >1.5 million SARS-CoV-2 sequences were submitted to GenBank. The initial version (v1.0) of the VADR (Viral Annotation DefineR) software package that GenBank uses to automatically validate and annotate incoming viral sequences is too slow and memory intensive to process many thousands of SARS-CoV-2 sequences in a reasonable amount of time. Additionally, long stretches of ambiguous N nucleotides, which are common in many SARS-CoV-2 sequences, prevent VADR from accurate validation and annotation. VADR has been updated to more accurately and rapidly annotate SARS-CoV-2 sequences. Stretches of consecutive Ns are now identified and temporarily replaced with expected nucleotides to facilitate processing, and the slowest steps have been overhauled using
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.