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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.


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.

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