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fastq-dump is a tool for downloading sequencing reads from NCBI’s Sequence Read Archive (SRA). These sequence reads will be downloaded as FASTQ files. How these FASTQ files are formatted depends on the fastq-dump options used.

Downloading reads from the SRA using fastq-dump

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

$ fastq-dump --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip --outdir path/to/reads/ SRR_ID

In this command…

  1. --gzip: Compress output using gzip. Gzip archived reads can be read directly by bowtie2.
  2. --skip-technical: Dump only biological reads, skip the technical reads.
  3. --readids or -I: Append read ID after spot ID as ‘’. With this flag, one sequence gets appended the ID .1 and the other .2. Without this option, pair-ended reads will have identical IDs.
  4. --read-filter pass: Only returns reads that pass filtering (without Ns).
  5. --dumpbase or -B: Formats sequence using base space (default for other than SOLiD). Included to avoid colourspace (in which pairs of bases are represented by numbers).
  6. --split-3 separates the reads into left and right ends. If there is a left end without a matching right end, or a right end without a matching left end, they will be put in a single file.
  7. --clip or -W: Some of the sequences in the SRA contain tags that need to be removed. This will remove those sequences.
  8. --outdir or -O: (Optional) Output directory, default is current working directory.
  9. SRR_ID: This is is the ID of the run from SRA to be downloaded. This ID begins with “SRR” and is followed by around seven digits (e.g. SRA1234567).

Other options that can be used instead of --split-3:

  1. --split-files splits the FASTQ reads into two files: one file for mate 1s (...1), and another for mate 2s (..._2). This option will not mateless pairs into a third file.
  2. --split-spot splits the FASTQ reads into two (mate 1s and mate 2s) within one file. --split-spot gives you an 8-line fastq format where forward precedes reverse (see


In this demo, fastq-dump is used to download compressed FASTQ reads.


Further reading

  1. Rob Edward’s notes on fastq-dump: