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illumina dump help

Guest on 11th July 2022 02:26:35 AM

  1.  
  2. Usage:
  3.   illumina-dump [options] [ -A ] <accession>
  4.   illumina-dump [options] <path>
  5.  
  6.         -A, --accession             Accession.
  7.  
  8. Options:
  9.  
  10.         -D, --table-path            Path to accession data.
  11.         -O, --outdir                Output directory. Default: '.'
  12.         -N, --minSpotId             Minimum spot id to output.
  13.         -X, --maxSpotId             Maximum spot id to output.
  14.         -G, --spot-group            Split into files by SPOT_GROUP (member).
  15.         -T, --group-in-dirs         Split into subdirectories instead of files.
  16.         -K, --keep-empty-files      Do not delete empty files.
  17.         -L, --log-level             Logging level: fatal|sys|int|err|warn|info. Default: info
  18.         -+, --debug                 debug: APP|KFS|XML|VDB|SRA|REF|LEGREF. Default: APP
  19.         -H, --help                  Prints this message.
  20.  
  21. Format options:
  22.  
  23.         -r, --read                  Output READ: "seq". Default: on
  24.         -q, --qual1                 Output QUALITY, into single (1) or multiple (2) files: "qcal". Default: 1
  25.         -p, --qual4                 Output full QUALITY: "prb". Default: off
  26.         -i, --intensity             Output INTENSITY, if present: "int". Default: off
  27.         -n, --noise                 Output NOISE, if present: "nse". Default: off
  28.         -s, --signal                Output SIGNAL, if present: "sig2". Default: off
  29.         -qseq                       Output QSEQ format: "qseq". Default: off

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