The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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NCBI SRA Toolkit fastq-dump 2.3.4


fastq-dump

fastq-dump is a part of the NCBI SRA Toolkit. It converts archive files in the SRA format into FASTQ format suitable for downstream analysis.

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Although this app is still functional, it does not have the capability of working with the new SRRs or splitting FASTQ files for paired-end reads. If you need that functionality, please use the NCBI-SRA-Fastq-dump-2.8.1 app instead.

App Creator

Roger Barthelson

Quick Start

  • To use fastq-dump, upload your data in SRA format and then specify the SRA accession name represented by that file. Most of the time, the filename (such as SRR012345.lite.sra) gives this information.
  • Resources: documentation

Test Data

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > ncbi_sra_toolkit_fastq_dump

Input File(s)

Use SRR070570.lite.sra  as a test input file.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.

Output File(s)

Expect a FASTQ file named after the accession as output.

Related Tutorials

ChIPseq Using the iPlant Discovery Environment

Tool Source for App

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

 
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