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: September 16, 2010.
    • 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: October 6, 2011.
    • 1 Overview
    • 2 The Run Browser
    • 3 Installing the Toolkit
    • 4 Downloading SRA Format Data
    • 5 Converting SRA format data into FASTQ
    • 6 Converting SRA format data into SFF
    • 7 Converting SRA format data into Illumina Native Files
    • 8 Converting SRA format data into ABI-SOLiD Native Files
    • 9 Compression by Reference
    • Appendix A – Toolkit Compiled Binary Components
  • Aspera Transfer Guide
    Dima Beloslyudtsev.
    Created: May 11, 2009; Last Update: November 22, 2010.
    • Notice
    • 1 Overview
    • 2 Aspera
• Submitting to the SRA
  • Submission Quick Start Guide
    Created: February 9, 2010; Last Update: March 22, 2012.
    • 1 Steps for SRA Submission
    • 2 Login
    • 3 Creating a New Submission
    • 4 Study
    • 5 Setting a Submission Release Date
    • 6 Status
    • 7 Sample
    • 8 Experiment
    • 9 Run
    • 10 Data Transfer
  • Submission Guide
    Created: January 13, 2009; Last Update: January 20, 2012.
    • 1 Overview
    • 2 Terms of Usage
    • 3 Data Model
    • 4 Obtaining NCBI Accounts Needed for Submission
    • 5 Submitting Data
    • 6 Tracking Submissions
    • 7 Preparing Submissions
    • 8 Preparing Metadata
    • 9 Managing Existing Submissions
    • 10 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: October 22, 2010.
    • 1 Overview
    • 2 Input Formats
    • 3 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
• 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: February 9, 2012; Last Update: May 10, 2012.
    • Overview
    • Design
    • Use Cases
    • Examples
    • Submission Considerations
    • Exchange Considerations