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fasterq-dump is a tool for downloading sequencing reads from NCBI’s Sequence Read Archive (SRA). These sequence reads will be downloaded as FASTQ files. fasterq-dump is a newer, streamlined alternative to fastq-dump; both of these programs are a part of sra-tools.

fasterq-dump vs fastq-dump

Here are a few of the differences between fastq-dump and fasterq-dump:

  1. In fastq-dump, the flag --split-3 is required to separate paired reads into left and right ends. This is the default setting in fasterq-dump.
  2. The fastq-dump flag --skip-technical is no longer required to skip technical reads in fasterq-dump. Instead, the flag --include-technical is required to include technical reads when using fasterq-dump.
  3. There is no --gzip or --bzip2 flag in fasterq-dump to download compressed reads with fasterq-dump. However, FASTQ files downloaded using fasterq-dump can still be subsequently compressed.

The following commands are equivalent, but will be executed faster using fasterq-dump:

$ fastq-dump SRR_ID --split-3 --skip-technical
$ fasterq-dump SRR_ID

Downloading reads from the SRA using fasterq-dump

In this example, we want to download FASTQ reads for a mate-pair library.

fastq-dump --threads n --progress SRR_ID

In this command…

  1. --threads specifies the number (n) processors/threads to be used.
  2. --progress is an optional argument that displays a progress bar when the reads are being downloaded.
  3. SRR_ID is the ID of the run from the SRA to be downloaded. This ID begins with “SRR” and is followed by around seven digits (e.g. SRA1234567).


In this video, fasterq-dump is used to download Saccharomyces cerevisiae RNAseq reads from the SRA.


See also


  1. How to use fasterq-dump from the sra-tools wiki on GitHub