Tool: fastq-dump

View the Project on GitHub ncbi/sra-tools

Usage

Frequently Used Options

General

  • -h |
  • -V |
  • --help
  • --version
  • Displays ALL options, general usage, and version information.
  • Display the version of the program.

Data Formatting




  • -I |
  • -F |
  • -C |
  • -B |
  • -Q |
  • --split-files
  • --split-spot
  • --fasta < [line width] >
  • --readids
  • --origfmt
  • --dumpcs < [cskey] >
  • --dumpbase
  • --offset < integer >
  • Dump each read into separate file. Files will receive suffix corresponding to read number.
  • Split spots into individual reads.
  • FASTA only, no qualities. Optional line wrap width (set to zero for no wrapping).
  • Append read id after spot id as 'accession.spot.readid' on defline.
  • Defline contains only original sequence name.
  • Formats sequence using color space (default for SOLiD). "cskey" may be specified for translation.
  • Formats sequence using base space (default for other than SOLiD).
  • Offset to use for ASCII quality scores. Default is 33 ("!").

Filtering

  • -N |
  • -X |
  • -M |



  • --minSpotId < rowid >
  • --maxSpotId < rowid >
  • --minReadLen < len >
  • --skip-technical
  • --aligned
  • --unaligned
  • Minimum spot id to be dumped. Use with "X" to dump a range.
  • Maximum spot id to be dumped. Use with "N" to dump a range.
  • Filter by sequence length >= < len >
  • Dump only biological reads.
  • Dump only aligned sequences. Aligned datasets only; see sra-stat.
  • Dump only unaligned sequences. Will dump all for unaligned datasets.

Workflow and piping

  • -O |
  • -Z |


  • --outdir < path >
  • --stdout
  • --gzip
  • --bzip2
  • Output directory, default is current working directory ('.').
  • Output to stdout, all split data become joined into single stream.
  • Compress output using gzip.
  • Compress output using bzip2.

Usage Examples

Possible errors and their solutions