fasterq-dump

Reference Code backup Executable files

Extract data in FASTQ- or FASTA-format from SRA-accessions

Category

Fetch Data

Usage

fasterq-dump <accession> [options]

Manual

fasterq-dump is the successor to the older fastq-dump tool, but faster. However: it is not a drop-in replacement, options and defaults are different.

Required arguments

fasterq-dump requires one of the following arguments

  • path: Path(s) to the .sra file(s)
  • accession: SRA accession ID.

Options

  • -o, --outfile: output-file
  • -O, --outdir: output-dir
  • -b, --bufsize: size of file-buffer (default=1MB)
  • -c, --curcache: size of cursor-cache (default=10MB)
  • -m, --mem: memory limit for sorting (default=100MB)
  • -t, --temp: where to put temp files (default=current directory)
  • -e, --threads: how many thread (default=6)
  • -p, --progress: show progress
  • -x, --details: print details
  • -s, --split-spot: split spots into reads
  • -S, --split-files: write reads into different files
  • -3, --split-3: writes single reads in special file
  • --concatenate-reads: writes whole spots into one file
  • -Z, --stdout: print output to stdout
  • -f, --force: force to overwrite existing file(s)
  • --skip-technical: skip technical reads
  • --include-technical: include technical reads
  • -M, --min-read-len: filter by sequence-len
  • --table: which seq-table to use in case of pacbio
  • -B, --bases: filter by bases
  • -A, --append: append to output-file
  • --fasta: produce FASTA output
  • --fasta-unsorted: produce FASTA output, unsorted
  • --seq-defline: custom defline for sequence:
    • $ac=accession
    • $sn=spot-name
    • $sg=spot-group
    • $si=spot-id
    • $ri=read-id
    • $rl=read-length
  • --qual-defline: custom defline for qualities: same as --seq-defline
  • -U, --only-unaligned: process only unaligned reads
  • -a, --only-aligned: process only aligned reads
  • -l, --row-limit: limit rowcount per thread
  • --disk-limit: explicitly set disk-limit
  • --disk-limit-tmp: explicitly set disk-limit for temp files
  • --size-check: switch to control:
    • on: perform size-check (default)
    • off: do not perform size-check
    • only: perform size-check only
  • --ngc PATH: PATH to ngc file
  • -h, --help: Output brief explanation for the program.
  • -V, --version: Display the version of the program then quit.
  • -L, --log-level level: Logging level as number or enum string. One of (fatal, sys, int, err, warn, info, debug) or (0-6) Current/default is warn
  • -v, --verbose: Increase the verbosity of the program status messages. Use multiple times for more verbosity. Negates quiet.
  • -q, --quiet: Turn off all status messages for the program. Negated by verbose.
  • --option-file file: Read more options and parameters from the file.

Example

Download a SRA file and extract fastq files (Note: running fasterq-dump without prefetch is slow, please refer to the Protocols section for optimal solutions):

fasterq-dump SRR000001

Already have a local SRA file, and use faster-dump to extract fastq files from the local file/folder:

fasterq-dump ~/data/SRR000001

 

Protocols using this tool

Download Fastq files from NCBI SRA database

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