Data Files and Formats
What File Formats Can I Submit?
The accepted format depends on the type of data.
Raw reads: FASTQ, BAM and CRAM, plus some platform-specific native formats. BAM or CRAM is recommended.
Genome and transcriptome assemblies: FASTA, or EMBL flat file where the assembly carries functional annotation.
Annotated sequences: EMBL flat file, or the TSV annotation templates.
See Preparing Files for Submission for the full requirements for each format, including file naming, compression and checksums.
How Do I Submit My Data?
There are three submission routes, and which you can use depends on the data type.
Interactive: fill in web forms in the Webin Portal, and download template spreadsheets to complete offline and upload. This is usually the most accessible route.
Programmatic: prepare your submission as XML or JSON documents and send them to ENA with a program such as cURL, or through the Webin Portal.
Webin-CLI: ENA’s command-line program, which validates your submission fully before it completes. It gives you the most control, and is required for assemblies and targeted sequences.
Raw reads can be submitted by any of the three. See Submission Options for reads, or Getting Started for the matrix of which route applies to each data type.
Can I Submit Oxford Nanopore POD5 Files?
No. POD5 is not currently supported, and ENA cannot accept submissions in that format while its longer-term approach to Oxford Nanopore native formats is under review.
Submit Oxford Nanopore reads as FASTQ instead. BAM is also accepted, for either aligned or unaligned reads.
See Oxford Nanopore.
To be told if this position changes, subscribe to the ena-announce mailing list.
I Have Uploaded My Files — Is That Enough To Submit Them?
No. The Webin upload area only stages your files; it does not submit anything. Copying files there by FTP, Aspera or any other means leaves them unsubmitted until you complete a submission that references them.
Assemblies and targeted sequences must be submitted with Webin-CLI, which performs the validation and processing those routes require. Reads can be submitted interactively, programmatically or with Webin-CLI.
To confirm an assembly submission succeeded, open the ‘Analyses Report’ in the Webin Portal; the assigned GCA and contig accessions appear in the analysis processing report.
My Upload Fails To Authenticate, But I Can Log In To Webin
When the Webin Portal accepts your credentials in a browser but FTP, Aspera or Webin-CLI uploads fail to authenticate, the cause is usually the network path rather than the credentials.
Retry the upload — transfer problems are occasionally transient.
Try Aspera instead of FTP, or FTP instead of Aspera.
Try from a machine outside your institutional or HPC network. If it works elsewhere, the restriction is on your network, and Configuring Your Firewall For ENA Upload lists the ports and addresses your IT department needs to permit.
If network access is not the cause, contact the ENA helpdesk with the exact error message and any transfer logs.