Usage:
fastq-dump [options] [ -A ]
fastq-dump [options]
-A, --accession Accession.
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 name).
-GL, --spot-group-list [name,[name...]] Filter by SPOT_GROUP (member).
-R, --read-filter [pass|reject|criteria|redacted] Split into files by READ_FILTER value, optional filter by a value.
-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.
-H, --help Prints this message.
Format options:
-M, --minReadLen Minimum read length to output. Default: 25
-W, --noclip Do not clip quality left and right for spot.
-F, --origfmt Excludes SRR accession & length on defline.
-C, --dumpcs [cskey] Dump color space sequence (default for ABI SOLID), single letter color space key is optional.
-B, --dumpbase Dump base sequence (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.
-TR, --dump-technical Include technical reads.
-SF, --complete Dump ALL reads in a single file.
-DB, --defline-seq sequence defline format specification. String of characters and/or variables.
Variables are one of:
$ac - accession, $si - spot id, $sn - spot name, $sg - spot group (barcode),
$sl - spot length in bases, $ri - read id, $rn - read name, $rl - read length in bases.
'[]' could be used for an optional output: if all variables in [] yield empty values whole group is not printed.
Empty value is empty string or 0 for numeric variables.
Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty
-DQ, --defline-qual quailty defline format specification. If -DB is provided but -DQommitted, -DB value is used.
-HS, --helicos Helicos style.
-FA, --fasta Fasta only, no qualities.
-alt [n] alternative formatting version [1].
Version: 2.0.4