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
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