SRA Handbook Last Updated: 2016 Jan 14 National Center for Biotechnology Information (US) Bethesda (MD) National Center for Biotechnology Information (US), Bethesda (MD) NLM Citation: SRA Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. iii This documentation provides an overview and help manual for the Sequence Read Archive (SRA) at the National Center for Biotechnology Information. iv SRA Handbook Table of Contents Introduction to SRA................................................................................................................................. 1 Concepts ............................................................................................................................................................. 3 Overview......................................................................................................................................................... 3 Concepts.......................................................................................................................................................... 3 Overview........................................................................................................................................................... 9 An Introduction to the Sequence Read Archive...................................................................................... 9 Terms of Usage .............................................................................................................................................. 9 SRA Features .................................................................................................................................................. 11 SRA Architecture ........................................................................................................................................... 14 SRA Data Structure ....................................................................................................................................... 17 The Necessity of Archival Data Storage .................................................................................................. 18 SRA Future Developments ........................................................................................................................... 19 Using the SRA............................................................................................................................................... 21 Download Guide........................................................................................................................................... 23 Overview......................................................................................................................................................... 23 Download with Prefetch............................................................................................................................... 24 The Run Browser............................................................................................................................................ 25 SRA BLAST...................................................................................................................................................... 28 Direct downloading of fasta and fastq format ....................................................................................... 30 Downloading metadata associated with SRA data files....................................................................... 31 Aspera Transfer Guide.............................................................................................................................. 33 Notice .............................................................................................................................................................. 33 Overview......................................................................................................................................................... 33 Aspera ............................................................................................................................................................. 33 Using ascp to Download by Command Line........................................................................................... 35 Using ascp to Upload by Command Line................................................................................................ 36 Requirements.................................................................................................................................................. 37 Contents v Troubleshooting.............................................................................................................................................. 37 Submitting to the SRA.......................................................................................................................... 39 Submission Quick Start Guide ............................................................................................................. 41 Steps for SRA Submission ........................................................................................................................... 41 BioProject ........................................................................................................................................................ 41 BioSample....................................................................................................................................................... 41 Login to the Sequence Read Archive ........................................................................................................ 43 Creating a New Submission....................................................................................................................... 43 Setting a Submission Release Date ........................................................................................................... 43 Status................................................................................................................................................................ 46 Experiment...................................................................................................................................................... 46 Links and Attributes....................................................................................................................................... 50 Run.................................................................................................................................................................... 53 Submission Checklist .................................................................................................................................... 55 Data Transfer.................................................................................................................................................. 55 Establishing a Center Account with SRA.................................................................................................. 56 SRA Batch Submission Guide................................................................................................................ 57 Prerequisites for SRA Submission .............................................................................................................. 57 BioProject ........................................................................................................................................................ 57 Creating a New Submission....................................................................................................................... 57 Additional Details.......................................................................................................................................... 59 Data Transfer.................................................................................................................................................. 62 Submitting Sequence Data for a dbGaP project....................................................................... 63 Steps to submitting read data for a dbGaP study to SRA.................................................................... 63 Submission Information ............................................................................................................................... 63 Protected Data Transmission....................................................................................................................... 64 SRA Submission Telemetry ..................................................................................................................... 67 Overview......................................................................................................................................................... 67 SRA Quick Start Guide................................................................................................................................ 67 vi SRA Handbook Submission Model......................................................................................................................................... 67 Interactive Telemetry ..................................................................................................................................... 67 Batch Telemetry.............................................................................................................................................. 69 Tools and Methods