Contents

• Introduction to SRA
  • Concepts
    Created: January 13, 2009; Last Update: September 16, 2010.
    • 1 Overview
    • 2 Concepts
  • Overview
    Created: May 1, 2009; Last Update: January 14, 2013.
    • 1 An Introduction to the Sequence Read Archive
    • 2 SRA Features
    • 3 SRA Architecture
    • 4 SRA Data Structure
    • 5 The Necessity of Archival Data Storage
    • 6 SRA Future Developments
• Using the SRA
  • Download Guide
    Created: September 9, 2009; Last Update: January 7, 2013.
    • Overview
    • The Run Browser
    • Using SRA Data
    • Downloading SRA Data
    • Reference Compression
  • Aspera Transfer Guide
    Dima Beloslyudtsev.
    Created: May 11, 2009; Last Update: November 22, 2010.
    • Notice
    • Overview
    • Aspera
• Submitting to the SRA
  • Submission Quick Start Guide
    Created: February 9, 2010; Last Update: May 20, 2013.
    • Steps for SRA Submission
    • BioProject
    • BioSample
    • Login to the Sequence Read Archive
    • Creating a New Submission
    • Setting a Submission Release Date
    • Status
    • Experiment
    • Run
    • Submission Checklist
    • Data Transfer
  • Submitting Sequence Data for a dbGaP project
    • Steps to submitting read data for a dbGaP study to SRA.
    • Submission Information
    • Protected Data Transmission
  • Submission Guide
    Created: January 13, 2009; Last Update: May 15, 2013.
    • Overview
    • Terms of Usage
    • Data Model
    • Obtaining NCBI Accounts Needed for Submission
    • Submitting Data
    • Tracking Submissions
    • Preparing Submissions
    • Preparing Metadata
    • Managing Existing Submissions
    • Tracking Submissions
  • SRA Submission Telemetry
    Created: March 12, 2012; Last Update: March 12, 2012.
    • Overview
    • SRA Quick Start Guide
    • Submission Model
    • Interactive Telemetry
    • Batch Telemetry
    • Tools and Methods
  • File Format Guide
    Created: September 23, 2009; Last Update: January 14, 2013.
    • Overview
    • Input Formats
    • Understanding Variants
  • Analysis Submission Guide
    Created: April 25, 2010; Last Update: March 2, 2011.
    • 1 Overview
    • 2 Data Model
    • 3 Reference Alignment
    • 4 BAM File Format
  • Submission Maintenance Guide
    Created: March 30, 2012; Last Update: May 15, 2013.
    • Overview
    • Interactive Update and Maintenance of a Submission
    • Maintenance through XML
    • Parts of the Schema that are Blocked from Modification
    • Common Errors and Methods to Fix Them
• SRA XML Writer's Guide
  • SRA Glossary
    Created: May 12, 2011; Last Update: May 20, 2011.
    • 1 Overview
    • 2 Sample Descriptor
    • 3 Library Descriptor
    • 4 Spot Descriptor
    • 5 Gap Descriptor
    • 6 Platform Descriptor
    • 7 Processing Descriptor
  • Using the SRA Data Block Descriptor
    Created: October 21, 2009; Last Update: September 16, 2010.
    • 1 Overview
    • 2 DATA_BLOCK Descriptor Attributes
    • 3 FILE Descriptor Attributes
    • 4 Implications for Loader Design
  • SRA Barcoding Guide
    Created: March 10, 2010; Last Update: September 24, 2010.
    • 1 Overview
    • 2 Use Cases
    • 3 Features
    • 4 Data Preparation
  • Using the SRA Identifier Block
    Created: August 3, 2012; Last Update: September 18, 2012.
    • Overview
    • Design
    • Use Cases
    • Submission Considerations
    • Exchange Considerations