
Usage:
  fastq-dump [options] <path>

Options:
  -D, --table-path            Path to accession data.
  -O, --outdir                Output directory. Default: '.'
  -N, --minSpotId             Minimum spot id to output.
  -X, --maxSpotId             Maximum spot id to output.
  -G, --spot-group            Split into files by SPOT_GROUP (member).
  -T, --group-in-dirs         Split into subdirectories instead of files.
  -K, --keep-empty-files      Do not delete empty files.
  -L, --log-level             Logging level: fatal|sys|int|err|warn|info.
                                [default: info]
  -+, --debug <level>         one of APP|KFS|XML|VDB|SRA|REF|LEGREF.
                                [default: APP]
  -H, --help                  Prints this message.

Format options:
  -M, --minReadLen            Minimum read length to output.
                                [default: 25]
  -W, --noclip                Do not clip quality right for spot.
  -F, --origfmt               Excludes SRR accession & length on defline.
  -C, --dumpcs [<cskey>]      Dump color space sequence.
                                [enabled by default for ABI SOLID]
                                [single letter color space key is optional]
  -B, --dumpbase              Dump base sequence.
                                [enabled by default for other than ABI SOLID]
  -Q, --offset                Offset to use for quality conversion.
                                [default: 33]
  -I, --readids               Append read id after spot id as
                                '<accession>.<spot>.<readid>' on defline.
  -E, --no-qual-filter        Disable filtering by leading/trailng low quality.
  -SF, --complete             Dump ALL reads in a single file.
  -DB, --defline-seq          Sequence defline format specification;
                              string of characters and/or variables.
  -DQ, --defline-qual         quailty defline format specification.
                                If -DB is provided but -DQ ommitted,
                                -DB value is used.
  -alt [n]                    alternative formatting version [1].

Defline substitution variables:
  '$ac'                       accession
  '$si'                       spot id
  '$sn'                       spot name
  '$sg'                       spot group (member/barcode)
  '$sl'                       spot length in bases
  '$ri'                       read id
  '$rn'                       read name
  '$rl'                       read length in bases.

  Substitution variables begin with a '$' character followed by a two
  character symbol, e.g. 'ac'. '[]' could be used for an optional output:
  if all variables in [] yield empty values whole group is not printed.
    Empty value is empty string or 0 for numeric variables.
    Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty

