fastq-dump help

    Usage:
      fastq-dump [options] [ -A ] <accession>
      fastq-dump [options] <path>

    INPUT
      -A|--accession <accession>       Replaces accession derived from <path> in filename(s) and deflines
      --table <table-name>             (New) Table name within SRA format, default is SEQUENCE

    PROCESSING

    Read Splitting                     Sequence data may be used as raw or split into individual reads
      --split-spot                     Split spots into individual reads

    Full Spot Filters                  Applied to the full spot independently of --split-spot
      -N|--minSpotId <rowid>           Minimum spot id
      -X|--maxSpotId <rowid>           Maximum spot id
      --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...]
      -W|--clip                        Apply left and right clips

    Common Filters                     Applied to spots when --split-spot is not set, otherwise - to individual reads
      -M|--minReadLen <len>            Filter by sequence length >= <len>
      -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                       optionally filter by a value: pass|reject|criteria|redacted
      -E|--qual-filter                 Filter used in early 1K Genomes data:
                                       no sequences starting or ending with >= 10N

    Filters for individual reads       Applied only with --split-spot set
      --skip-technical                 Dump only biological reads

    OUTPUT
      -O|--outdir <path>               Output directory, default is '.'

    Multiple File Options              Setting this options will produce more than 1 file, which will be suffixed by splitting criteria.
      --split-files                    Dump each read into a separate file.Files will received suffix corresponding to read number
      --split-3                        Legacy 3-file splitting for mate-pairs:
                                       First 2 biological reads satisfying dumping conditions
                                       are placed in files *_1.fastq and *_2.fastq
                                       If only 1 biological read is dumpable - it is placed in *.fastq
                                       Biological reads 3 and above are ignored.
      -G|--spot-group                  Split into files by SPOT_GROUP (member name)
      -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                       optionally filter by a value: pass|reject|criteria|redacted
      -T|--group-in-dirs               Split into subdirectories instead of files
      -K|--keep-empty-files            Do not delete empty files

    FORMATTING

    Sequence
      -C|--dumpcs <[cskey]>            Formats sequence in color space (default for SOLiD),cskey may be specified for translation
      -B|--dumpbase                    Formats sequence in base sequence (default for other than SOLiD).

    Quality
      -Q|--offset <integer>            Offset to use for quality conversion, default is 33
      --fasta                          Fasta only, no qualities

    Defline
      -F|--origfmt                     Defline contains only original sequence name
      -I|--readids                     Append read id after spot id as 'accession.spot.readid' on defline
      --helicos                        Helicos style defline
      --defline-seq <fmt>              Defline format specification for sequence.
      --defline-qual <fmt>             Defline format specification for quailty.
                                       <fmt> is string of characters and/or variables. Variables could be are one of:
                                          $ac - accession, $si - spot id, $sn - spot name, $sg - spot group (barcode),
                                          $sl - spot length in bases, $ri - read number, $rn - read name, $rl - read length in bases.
                                       '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed.
                                       Empty value is empty string or 0 for numeric variables.
                                       Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty

    OTHER:
      -h|--help                        Output a brief explantion 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) or (0-5)
                                       Current/default is warn
      -v|--verbose                     Increase the verbosity level of the program
                                       Use multiple times for more verbosity