Category
Fetch Data
Usage
prefetch [options] <SRA accession>
Manual
Required arguments
SRA accession: The Sequence Read Archive (SRA) accession identifier(s) of the data to download.
Options
- -T or --type value: Specify the file type to download. Default: sra.
- -t or --transport http|fasp|both: Choose the transport method: fasp, http, or both [default]. "Both" first try fasp (ascp), if fails, use http instead.
- --location value: Specify the location of the data.
- -N or --min-size size: Minimum file size to download in KB (inclusive).
- -X or --max-size size: Maximum file size to download in KB (exclusive). Default: 20G.
- -f or --force yes|no|all|ALL: Force object download. Options: no [default], yes, all, ALL.
- -r or --resume yes|no: Resume partial downloads. Options: no, yes [default].
- -C or --verify yes|no: Verify after download. Options: no, yes [default].
- -p or --progress: Show download progress.
- -H or --heartbeat value: Display download progress at specified time intervals. Default: 1.
- --eliminate-quals: Don't download QUALITY column.
- -c or --check-all: Double-check all refseqs.
- -S or --check-rs yes|no|smart: Check for refseqs in downloaded files. Options: no, yes, smart [default].
- -o or --order kart|size: Kart prefetch order when downloading. Options: kart, size [default].
- -R or --rows rows: Kart rows to download (default all). Row list should be ordered.
- --perm PATH: PATH to JWT cart file.
- --ngc PATH: PATH to NGC file.
- --cart PATH: To read kart file.
- -a or --ascp-path ascp-binary|private-key-file: Path to ascp program and private key file.
- --ascp-options value: Arbitrary options to pass to ascp command line.
- -o or --output-file FILE: Write file to FILE when downloading single file.
- -O or --output-directory DIRECTORY: Save files to DIRECTORY.
Examples
To download SRA files and their dependencies, you can use a command like this:
prefetch SRA123456
Protocols using this tool
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