Submitting data to SRA
Introduction
The European Nucleotide Archive (ENA) accepts both sequence read and analysis (e.g. BAM alignment and VCF variation) data generated by next-generation sequencing methodologies such as 454, Illumina Genome Analyzer and ABI SOLiD into the Sequence Read Archive (SRA). ENA works in close collaboration with the NCBI and DDBJ as part of the International Nucleotide Sequence Database Collaboration (INSDC). All submitted public data is exchanged between the partners on a daily basis.
For all questions and enquiries please contact datasubs@ebi.ac.uk.
Public access data
SRA only accepts data which is intended for public release. Controlled access data should be submitted to European Genome-phenome Archive (EGA).
During the submission processing submitters should define whether the submitted metadata and data should become immediately public or if they should remain confidential for a period of no more than two years. Once data has been released it can be withdrawn from public access only in exceptional circumstances.
Please contact datasubs@ebi.ac.uk to request for a submission account.
Controlled access data
The European Genome-phenome Archive (EGA) accepts submissions of next-generation sequencing data that should be kept under controlled access. Submitted data files will always remain under controlled access. Associated SRA metadata will only be made public after manual curation to gurantee that no sensitive information is accidentially revealed.
Please contact ega-helpdesk@ebi.ac.uk to request for a submission account.
SRA data object model
SRA data model contains the following objects:
- Study: information about the sequencing project
- Sample: information about the sequenced samples
- Experiment: information about the libraries, platform; associated with study, sample(s) and run(s)
- Run: contains the raw data files
- Analysis: contains the analysis data files; associated with study, sample and run objects
- Submission: information about the submission actions include release date
Submitting public access data using SRA Webin
SRA Webin is the recommended submission interface for most submitters:
SRA Webin provides an intuitive way to submit the required metadata and the data files. Large sequencing centers should consider using the SRA REST service, which can be integrated programatically with LIMS systems.
Two SRA Webin video tutorials are available:
General information about the SRA Webin submission process
Practical tutorial of the SRA Webin submission process
Submission process
Please contact datasubs@ebi.ac.uk to request for a submission account. This grants you access to SRA Webin:
Please note that data files must be uploaded to your drop box using FTP or Aspera. Information about acceptable data formats is available here.
In SRA Webin:
- Go to the New Submission page
- Choose sequence read submission and provide release date
- Provide study information
- Provide sample information
- Provide instrument platform, library and data file information
Please do not use SRA Webin to submit quantative metagenomic studies. The system does not currently capture sufficient information to comply with the GSC (genomic standards consortium) standards for reporting genoming and metagenomic sequences. Instead, The EBI Metagenomics team will broker your submission for you: http://www.ebi.ac.uk/metagenomics/.
Please do not use SRA Webin to submit quantative expression based studies such as RNA-Seq and CHIP-Seq yet. The system does not currently capture sufficient information for MIAME compliance. Array Express will broker your submission for you. Please use their MAGE-TAB submission system: http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi.
SRA submission services are also available from third parties, including the myRDP SRA Prepkit (https://pyro.cme.msu.edu/sra/login.spr) and the ISA Infrastructure (http://isatab.sourceforge.net/).
For all questions and enquiries please contact datasubs@ebi.ac.uk.
Submitting public and controlled access data using SRA REST
We recommend that large scale submitters integrate the SRA and EGA submission process with their LIMS systems. We provide a RESTful submission tool which can be used to submit study, sample, experiment, run, analysis, EGA DAC, EGA policy, EGA dataset XML objects and data files. Advice on preparing SRA XML files required by the service is available here.
The SRA REST submission tool provides immediate validation and SRA object accessioning and can be used for repeated regular SRA submissions. All SRA submitters with submission accounts can take advantage of this service. We also provide a simple web form which can be used to explore and use the SRA REST submission interface.
Please note that data files must be uploaded to your drop box using FTP or Aspera. Information about acceptable data formats is available here.
It is also possible to update any SRA objects using the SRA REST service. The only exception are some limitations on updating data file related details. Advice on how to update SRA objects is available here.
For all questions and enquiries please contact datasubs@ebi.ac.uk.
Submission validation
All submitted SRA objects are validated prior accessioning. Detailed information about the validations is available here.
