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.
Here are a few of the differences between
fastq-dump, the flag
--split-3is required to separate paired reads into left and right ends. This is the default setting in
--skip-technicalis no longer required to skip technical reads in
fasterq-dump. Instead, the flag
--include-technicalis required to include technical reads when using
- There is no
fasterq-dumpto download compressed reads with
fasterq-dump. However, FASTQ files downloaded using
fasterq-dumpcan still be subsequently compressed.
The following commands are equivalent, but will be executed faster using
$ fastq-dump SRR_ID --split-3 --skip-technical $ fasterq-dump SRR_ID
In this example, we want to download FASTQ reads for a mate-pair library.
fastq-dump --threads n --progress SRR_ID
In this command…
--threadsspecifies the number (
n) processors/threads to be used.
--progressis an optional argument that displays a progress bar when the reads are being downloaded.
SRR_IDis 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.
In this video,
fasterq-dump is used to download Saccharomyces cerevisiae RNAseq reads from the SRA.