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
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
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