/usr/share/doc/sra-toolkit/help/txt/illumina-dump-help.txt is in sra-toolkit 2.1.7a-1ubuntu2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | Usage:
illumina-dump [options] [ -A ] <accession>
illumina-dump [options] <path>
-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).
-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 debug: APP|KFS|XML|VDB|SRA|REF|LEGREF. Default: APP
-H, --help Prints this message.
Format options:
-r, --read Output READ: "seq". Default: on
-q, --qual1 Output QUALITY, into single (1) or multiple (2) files: "qcal". Default: 1
-p, --qual4 Output full QUALITY: "prb". Default: off
-i, --intensity Output INTENSITY, if present: "int". Default: off
-n, --noise Output NOISE, if present: "nse". Default: off
-s, --signal Output SIGNAL, if present: "sig2". Default: off
-qseq Output QSEQ format: "qseq". Default: off
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