ENA Submission Tool
Submission of nucleotide sequencing and metagenomics metadata: Integration with ENA web services API
Since version 1.7.8, ISAcreator supports submission of metadata to the European Bioinformatics Institute (EBI) European Nucleotide Archive (ENA) and Metagenomics portal (EMG). This functionality relies on ENA REST services and requires the user to register an account (either through ENA or EMG) and upload the data files before the submission of the metadata.
The ISAcreator File menu now contains an option to Submit to ENA. Once you opened the ISA-Tab files of your sequencing experiment, you can use this option to validate, convert to SRA-xml and submit to the ENA repository.
From the initial ENA submission screen you can choose to create a new submission or update an existing one.
Then, you can choose from the test, development or production servers from ENA to give the freedom to test your upload before doing it for real.
Next you need to enter your login details for the ENA Dropbox. Instructions on how to create an account for ENA are available here and for EBI Metagenomics are available here.
Finally, you can enter the SRA Centre Name, Broker Name and Lab Name (if different from the ones declared in the ISA-Tab files). You need to contact ENA to get these details.
When you press the Next button, the ISA-Tab files will be validated, converted to SRA-xml and submitted to ENA with the credentials provided. As stated above, the data files have to be previously uploaded to the ENA Dropbox using one of the data upload methods provided by ENA.
If validation, conversion or submission fail, you will be notified with an error screen detailing the problem. For example, this screen shows a submission failure as the data files were not previously uploaded:
If validation, conversion and submission are successful, you will see a screen with the accession numbers assigned at ENA for studies, experiments, runs and samples. See the example below.
Here you can see a video tutorial about the ENA submission.