New GenBank submission options for SARS-CoV-2 submitters

NCBI is pleased to announce ongoing enhancements to submission of SARS-CoV-2 assembled genomes to GenBank, including a streamlined workflow on the web and a new API option. Both new options mean that you can receive accessions for SARS-CoV-2 data submissions more quickly!

A streamlined workflow with improved interface and enhanced validation on both web and API saves you time and effort and, most importantly, makes it possible to get SARS-CoV-2 accession numbers and public release of data within hours. In addition, we automatically annotate all SARS-CoV-2 genomes to produce standardized, consistent annotation which saves you time and benefits researchers who find your data valuable.

Which option is right for you and your organization?

If you need a pipeline for frequent or large volume submissions, use the brand-new SARS-CoV-2 API. Contact us at to set up an account!

Otherwise, you can use the new SARS-CoV-2 submission wizard in the Submission Portal (Figure 1).

The option for SARS-CoV-2 appears under the question "What do your sequences contain?"
Figure 1. For SARS-CoV-2, click the Submission Portal link above to get started and select “severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” to upload your sequence., or go to the SARS-CoV-2 submission landing page for more information. The landing page also provides instructions for submitting unassembled, next-generation sequence reads to Sequence Read Archive (SRA).

There are two convenient approaches for uploading metadata in the wizard: uploading from a tab-delimited table or adding your data through an Excel-style editable table.

Tip: Submitters should use the isolate name format set by the ICTV and recommended here by the NCBI and SPHERES Open Genomics Consortium (Figure 2). Both formats shown are acceptable. However, do not mix formatted and non-formatted isolate types in a single submission.

Examples of source metadata
Figure 2. Examples of source metadata.

The new web submission tool for SARS-CoV-2 continues migrating all GenBank web submission to a single interface, as it moves SARS-CoV-2 submission to the same user-friendly, online tool for rRNA submissions, animal mitochondrial COX1 sequences, and certain other pathogenic viruses such as Influenza, Norovirus and Dengue.

NCBI is continually improving SARS-CoV-2 submission processing and welcomes your input! Contact us with feedback or questions.

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