Submitting read data

European Nucleotide Archive (ENA) accepts sequence reads and associated analyses. Once public, data submitted to ENA is exchanged between International Nucleotide Sequence Database Collaboration (INSDC) partners: NCBI and DDBJ.

If you have any questions regarding the submission process contact

Public access data

ENA accepts data submissions which are intended for public release. Controlled access data should be submitted to European Genome-phenome Archive (EGA).

During the submission process submitters have the opportunity to decide whether the submitted data should become immediately public or should remain confidential for up to two years. Once data has been publicly released it can be withdrawn from public access only in exceptional circumstances.

Controlled access data

Controlled access data should be submitted to the European Genome-phenome Archive (EGA). The decisions of who will be granted access to data resides with the submitter nominated Data Access Committee.

Please contact to request for an EGA submission account.

Supported read file formats

Please use one of the supported read file formats ... more infomation.

Registering a submission account

Submissions are made through a registered Webin submission account ... more information.

Uploading read files

Read files must be uploaded before they can be submitted using Webin ... more information.

Interactive submissions

  1. Login into Webin.
    Webin Login
  2. Go to the New Submission page.
    Webin New Submission Tab
  3. Upload data files
  4. Choose Submit sequence reads and experiments 
    Webin Submit Sequence Reads Choice
  5. Provide study information
  6. Provide sample information
  7. Provide experiment information and associate experiments with data files

Please do not use Webin to submit quantative expression based studies such as RNA-Seq and CHIP-Seq. For these types of experiments, please use Annotare to ensure MIAME compliance.

Programmatic submissions

Large sequencing centers and brokers are encouraged to submit programmatically through Webin to automate the submission process ... more information.

Third party submissions

Read data submission services are also available from third parties, including the ISA Infrastructure.

Metadata model

The Webin metadata model consists of several objects each of which can be submitted separately ... more information.

Fair use policy

ENA provides a permanent and comprehensive data repository for public domain sequence and associated information. Data being submitted into this system are routed through private data upload areas which users upload their data files. Upon submission instruction from the user through Webin files are validated and moved out of the data upload area into the archive.

The data upload areas are provided as a temporary storage in which data in transit are held and are not intended nor suitable for any longer term storage. Long-term storage is provided in the archive itself. Data can be released immediately following loading or can be held confidential prior to analysis and literature publication if required.

Under normal circumstances, we expect any given data file to remain in a data upload area for no longer than 2 months before the instruction is given to submit the file. In order to use storage efficiently, we limit usage of the data upload areas as described above and reserve the right to routinely remove any data files that persist in them for more than 2 months.

Latest ENA news

01 Jul 2015: ENA release 124
Release 124 of ENA's assembled/annotated sequences now available

20 Jun 2015: Sample Checklist Updates - June 2015
ENA are planning to update several sample metadata reporting checklists. Some of these changes have been carried out for harmonisation of attributes/fields between various checklist. Other changes were made to allow a standardised missing/null value reporting. All changes will come into effect as of 3rd August 2015.

03 Jun 2015: Changes to read data submission services 1st of October 2015
ENA will make a number of changes to submission services for raw sequence read data on first of October 2015. We continue to track an ever evolving landscape of available and preferred formats and introduce these changes with a view to overall simplification of the submission system to allow us to provide a more efficient service with faster turnaround.