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Fastq-dump

fastq-dump is a tool for downloading sequencing reads from NCBIā€™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 commandā€¦

  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 ā€˜accession.spot.readidā€™. 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 ā€œSRRā€ 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 https://www.biostars.org/p/178586/#258378).

Demonstration

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

asciicast

Further reading

  1. Rob Edwardā€™s notes on fastq-dump: https://edwards.sdsu.edu/research/fastq-dump/