Options for clc_quality_trim

usage: clc_quality_trim [options]
  Trim a read file based on quality.
  -h / --help: Display this message.
  -r <file> / --input <file>: Input read file. (Required)
  -q <file> / --quality <file>: Specify separate input quality file.
  -o <file> / --output <file>: Output read file (fasta or fastq format depending
    on name). (Required)
  -p <file>/ --paired <file>: Output file for pairs (fasta or fastq).
  -c <n> / --cutoff <n>: Set the minimum quality for a good nucleotide. (Default
  -b <n> / --badfraction <n>: Set the maximum fraction of bad nucleotides to
    define a good quality region. (Default 0.1)
  -l <n> / --lengthfraction <n>: Set the fraction of the read that must be of
     good quality. (Default 0.5)
  -m <n> / --minlength <n>: Set the minimum length of output reads. (Default 0)
  -n / --notrim: Do not trim the sequence, but replace bad quality with Ns
  -s / --colorspace: The data are from color space sequencing. This option
    moves the start trim one position to the left (see manual).
  -f <offset> / --qualityoffset <offset>: Set the ascii offset value in fastq
      files. If not specified, the offset is estimated by examining the input files.
  -i <file1> <file2> / --interleave <file1> <file2>: Interleave two sequence
     files with the same number of sequences. May be used instead of a single
     file following -r or -q.