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Sequence Read Archive (SRA)

SRA is an open access archive of minimally-processed read data from high throughput platforms.

What You Should Expect

Prepare the following information for your submission and be ready to:

  1. Provide a project name and description
  2. Choose the type or ‘package’ of your samples
  3. Provide sample metadata that is unique by sample
  4. Provide sequence metadata
  5. Upload your files

Watch a 10 min video tutorial.

For a new project, prepare the information that creates a BioProject.

Required information:

  1. Title
  2. Description

Optional information:

  1. Participants
  2. Grants: Required if your project was funded by a National Institutes of Health (NIH) grant

Important: The required BioProject and BioSample can be created during submission. You can also link an existing BioProject and BioSample with accession numbers.

For new samples, prepare the details that will serve as BioSamples' metadata for individual biological specimens (collection date, location, etc.).

  1. Select the ‘package’ that best fits your biological samples. Each package has a distinct set of required attributes which you can preview here.
  2. Each sample must have a unique set of attributes. Provide all required fields and any optional fields that apply to your samples.
  3. Add custom attributes to fully describe your samples and facilitate searching. You should submit at least one unique data file for each sample you create.

Prepare the following 'Library' information:

  1. Which BioSample should be linked to which file(s)
  2. Your library construction protocol
  3. Other metadata like unique library names, sequencing platform, and filetype.

Ensure the file name(s) you choose do not contain any sensitive information. File names as submitted appear publicly on the Google and AWS clouds.

Upload data files for your SRA submission. There are several options available:

  1. File upload via the web interface using HTTP or the Aspera Connect browser plugin
  2. FTP and Aspera on the command line
  3. Upload from Amazon S3 storage or Google Cloud Platform bucket

Please note that your uploaded file names should be an exact match to the file names listed on the 'Metadata' tab, including file extension.

Submit your sequence data on desktop. The desktop view allows you to easily:

  • Enter your information
  • Enter or upload metadata
  • Upload large source files
  • Review your submission

Email me a link to get started

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SRA FAQ

  • No, you can create a BioProject and BioSamples as part of your SRA Submission. Please indicate that you have not previously registered these objects when asked and the submission wizard will prompt you to enter that information along with the rest of your submission metadata.

  • Yes, you can release your data or update the release date from 'Manage data' tab. Select the BioProject related to the data you would like to release, then click the ‘Edit’ button next to ‘Release date.’ Follow the prompts there to update your release date.

  • To add data to an existing BioProject, please create a new SRA submission and enter the BioProject accession (looks like PRJNA#) when asked. This will ensure the new data is linked to the existing BioProject.

  • You can generate a reviewer metadata link from the 'Manage data' tab. From this interface, navigate to the BioProject page for the pertinent dataset, then click the 'Create Reviewer Link' button to the right of the BioProject accession near the top of the page. Share data with colleagues or your publisher's reviewer.

  • SRA users are able to see all the metadata describing your data files and they will be able to retrieve the original submitted files with their original file names. SRA users will also be able to retrieve the standardized SRA version of your data files.

  • Yes, you may collaborate on your submissions by using a submission group. Shared submission groups give multiple submitters access to submission data in the Submission Portal and Manage Data. A shared submission group consists of multiple NCBI accounts within the Submission Portal, all of which have permissions-based access to submissions associated with the group. Learn more.

  • SRA accepts data from all kinds of sequencing projects including clinically important studies that involve human subjects or their metagenomes, which may contain human sequences. These data often utilize NIH controlled access via dbGaP (the database of Genotypes and Phenotypes). Data submitters need to determine if their data is suitable for public distribution or if it needs controlled access. For further information, consult with institutional review boards and NIH Genomic Data Sharing Policy.

    It is the responsibility of submitting parties to ensure that they have appropriate consent for human sequence data to be distributed publicly without access controls. We encourage submitters to screen for and remove contaminating human reads from data files prior to submission. We also offer human contamination screening as a service available on request.

    For more information please email: sra@ncbi.nlm.nih.gov

  • Yes. If you plan to submit regularly, or submit a large volume of data, programmatic submissions is a suitable and efficient alternative.

    Start by contacting sra@ncbi.nlm.nih.gov with the subject "Center account creation for XML submissions." Please provide:

    • Suggested center abbreviation (16 char max)
    • Center name (full), center URL & mailing address (including country and postcode)
    • Phone number (main phone for center or lab)
    • Contact person (someone likely to remain at the location for an extended time)
    • Contact email (ideally a service account monitored by several people)
    • Whether you intend to submit via FTP or command line Aspera (ascp)

    A test area and a production area will be created. Deposit the XML file and related data files into a directory and follow the instructions SRA provides via email to indicate when files are ready to trigger the pipeline.

    Complete several successful tests before making a production submission. The SRA team will assist you.

    Important: The submission.xml file can link to either an existing BioProject/BioSamples or register new BioProject/BioSamples. The XML file is broken up into “Action” blocks and each “Action” is an instruction to the database referenced inside the “Action” block. Simple “Action” block for SRA: https://github.com/ncbi/submission-schema/blob/master/sra/samples/sra.submission.run.xml