Submit High-throughput Sequencing Reads to NCBI Sequence Read Archive (SRA)¶

Goal¶

This workflow enables CyVerse users to make submissions to the NCBI Sequence Read Archive (SRA). A submission included compressed sequenced files (FASTQ.gz, SFF.gz, and BAM.gz) and an XML metadata file, organized into a package. If you need to submit an alternative file format (HD5, SOLiD, and SRF) please email support@cyverse.org

Quickstart home
Create and organize an SRA submission package
- (Optional) Compress files in the CyVerse Data Store using gunzip
- Create SRA submission package and add sequence data
Record metadata and associate with SRA submission
Validate and submit package to SRA
- I. Validate Submission
- II. Send submission package to SRA
Confirm submission to SRA and fix errors
- If your SRA submission is successful
- If your SRA submission contains errors

Prerequisites¶

Note

To complete this tutorial, you must upload your FASTQ/SFF/BAM files to the CyVerse Data Store. See the Data Store Guide for instructions on how to upload your files (for example, using Cyberduck). Also, you will need detailed metadata about the sample being submitted ( e.g. collection/accession information, cell line/tissue metadata, etc.) and the sequencing platform used (e.g. library preparation strategy, sequencing instrument, etc.). These requirements will vary for the organism sequenced and are discussed in detail in the metadata section of this quickstart.

Downloads, access, and services¶

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download

CyVerse account You will need a CyVerse account to complete this exercise Register

NCBI Account Submissions will be sent to NCBI Register

Note

Register for an NCBI Account

If you do not have an NCBI account (you can check for an existing account logging in at https://www.ncbi.nlm.nih.gov/account/ ); register at https://www.ncbi.nlm.nih.gov/account/register/.

Platform(s)¶

We will use the following CyVerse platform(s):

Platform	Interface	Link	Platform Documentation	Quick Start
Data Store	GUI/Command line	Data Store	Data Store Manual	Guide
Discovery Environment	Web/Point-and-click	Discovery Environment	DE Manual	Guide

Input and example data¶

In order to complete this quickstart you will need to have the following inputs prepared

Input File(s)	Format	Preparation/Notes	Example Data
FastQ/SFF/BAM files	FastQ/SFF/BAM compressed (.gz/.bz2).	For additional details see the SRA File Format Guide	Sample truncated sample FastQ files

Fix or improve this documentation

On Github: Repo link
Send feedback: Tutorials@CyVerse.org

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