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 datasubs@ebi.ac.uk.

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 Once data has been publicly released it can be withdrawn from public access only in exceptional circumstances.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 ega-helpdesk@ebi.ac.uk 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 is a permanent and comprehensive data repository for public domain sequence and associated information. Data submitted into this system are routed transiently through users’ private data upload areas until such time as a submission instruction from the user, through his/her use of the Webin system, leads to the validation of the data and the movement of files from the data upload area into the ENA.

The data upload areas are provided as a temporary place in which data are held while in transit. As such, they are neither intended nor suitable for any longer-term storage of data. Such storage is provided in ENA itself. Once in ENA, data can be released immediately following submission or can be held confidential prior to analysis and literature publication if required.

We expect any given data file to remain in a data upload area for no longer than 2 months before the instruction is given by the user to submit the file. While we attempt to remind users of this policy at the 2 months time point we reserve the right to routinely delete any data files that persist in them for more than 2 months.

We place no absolute limit within the 2-month period on the total volume of user data that may exist in a data upload area at any one time and are keen to accommodate the largest submissions where possible. However, we strongly encourage continuous data submissions where files are uploaded and submitted in small patches of few Terabytes or less and expect that volumes would not exceed 10 Terabytes under normal circumstances. Users who expect to deviate from this pattern of usage are encouraged to contact us through datasubs@ebi.ac.uk at the earliest opportunity. Unexpected heavy use of the data upload areas may have an impact on other Webin users and we are grateful for users’ attention to this aspect of our fair use policy.