SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Submissions

Please see below for instructions on how to submit SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) data. If you have any queries or require assistance with your submission please contact us at: virus-dataflow@ebi.ac.uk.

Registering Studies

Data submissions to the ENA require that you register a study to contextualise and group your data. Details of how to do this can be found here: https://ena-docs.readthedocs.io/en/latest/submit/study.html. Please ensure you describe your study adequately, as well as provide an informative title.

Registering Samples

Having registered a study, please proceed to register your samples. Instructions for sample registration are found here: https://ena-docs.readthedocs.io/en/latest/submit/samples.html. As part of this process, you must select a sample checklist to describe metadata. The most appropriate checklist for Coronavirus submissions is the “ENA virus pathogen reporting standard checklist”. The attributes available in this checklist can be viewed here: https://www.ebi.ac.uk/ena/browser/view/ERC000033. Please use the organism name “Severe acute respiratory syndrome coronavirus 2”, the taxonomic ID 2697049 and please also provide a geographical location (as precise as possible).

Submitting Reads

After registering your study and samples, you can submit your read files along with experimental metadata. Instructions to submit reads are found here: https://ena-docs.readthedocs.io/en/latest/submit/reads.html.

Submitting Assemblies

If submitting assemblies, you must have registered a study and a sample beforehand. It is also advised that associated read data is also submitted. Instructions for assembly submission are found here: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html.

Submitting Targeted Sequences

If submitting targeted or annotated sequences, you must register a study as described above. Instructions for submitting sequence data are found here: https://ena-docs.readthedocs.io/en/latest/submit/sequence.html. As part of this process, if submitting annotated sequences, you must select an annotation checklist, found here: https://www.ebi.ac.uk/ena/submit/annotation-checklists. There are several virus-specific annotation checklists, with “Single Viral CDS” the most appropriate for complete or partial coding sequence from a viral gene. If your sequences do not fit the annotation checklists above please contact us at virus-dataflow@ebi.ac.uk.

If submitting single contig assemblies, or for any other support or issues around SARS-CoV-2 submissions please contact virus-dataflow@ebi.ac.uk.

Release of Data

Users are responsible for releasing data they submit to ENA. This is done by setting an appropriate release date, as detailed here: https://ena-docs.readthedocs.io/en/latest/faq/release.html#can-i-advance-postpone-the-release-date.