Are you looking for SARS-CoV-2 sequence data? Look no further! The NCBI Virus SARS-CoV-2 Data Hub now has an interactive data dashboard (Figure 1) that shows the collection location (country and US state), the date of collection, and the date of public availability for SARS-CoV-2 sequence data. You can view available nucleotide and protein sequences based on criteria you select and send these to a data table. You can further filter by normalized source information including sequence length, protein content, host, anatomical isolation source. The sequence records have links to related SRA records and publications in PubMed when available. You can download the data as FASTA-formatted sequences with customizable titles, accession lists, or as a table including data descriptors. See the help documentation for more details.
The sequences in NCBI Virus were submitted to members of the International Sequence Database Consortium (INSDC) – GenBank, EMBL, and DDBJ. This collaborative effort ensures that data is freely available to the scientific and public health communities where it can be used to understand the biology, evolution, and spread of SARS-CoV-2.
Figure 1. The NCBI Virus SARS-CoV-2 Data Hub Dashboard. You can narrow down sequence data using collection location, collection date, or the public release date. After making your selections, click “View results, Analyze, or Download” near the top of the page to see your dataset in the results table, which shows nucleotide, protein, and RefSeq sequences as well as associated metadata.
The NCBI Virus SARS-CoV-2 Data Hub is an NCBI Labs project that we are actively developing and may change rapidly. This resource supports open data and is available free on an easily-accessed web-based platform. Future enhancements to support SARS-CoV-2 research include:
- selecting sequences based on variations,
- normalization of protein and mature peptide annotation using VADR (Viral Annotation DefineR), as well as searching based on the normalized annotation, and
- additional new ways of identifying patterns in the data.
Our goal is to support our SARS-CoV-2 researchers and the broader virus research community in the best way possible! We would love your feedback on how NCBI Virus is currently meeting your research needs and how we can make it better. Please let us know what you think through the green ‘Feedback’ button at the bottom of any of our NCBI Virus pages or send a message to firstname.lastname@example.org.