Options for clc_overlap_reads 

usage: clc_overlap_reads <options>
  Join overlapping reads.
Options:
  -h / --help: Display this message
  -r <file> / --readfile <file>: Set the input read file (required)
  -i <file1> <file2> / --interleave <file1> <file2>: Interleave two input files.
      Use in place of input file name for -r option.
  -q <file> / --qualityfile <file>: Set a separate input quality file (may also
     be interleaved).
  -j <file> / --jointfile <file>: Set the output file for joint reads. Use a file
     name ending on ".fq" or ".fastq" for fastq output format. (required)
  -n <file> / --nonjointfile <file>: Set the output file for reads that were not
     joined.. Use a file name ending on ".fq" or ".fastq" for fastq output
     format
  -l <n> / --minlength <n>: Set the minimum length of output reads. Only applies
     to joint sequences. (Default 0)
  -o <n> / --minoverlap <n>: The minimum length of the overlap alignment between
     two reads (default 10).
  -s <n> / --similarity <n>: The minimum similarity of the overlap between two
     reads (default 0.9).
  -m <mode> / --mode <mode>: Set the joining mode to one of these:
     first: use the first read in the overlap region.
     second: use the second read in the overlap region.
     quality: use the highest quality nucleotide for each position. (default)
  -p <par> / --paired <par>: Set the paired read mode for the reads. <par> may
     be ff, fb (default), bf, or bb and sets the relative orientation of read
     one and two in a pair (f = forward, b = backward). Joint output is always
     in the forward direction starting with the first read of a pair.
  -x <n> / --mismatchcost <n>: Set the mismatch cost, match cost is always 1.
     (integer, minimum 1, default 2)
  -g <n> / --gapcost <n>: Set the gap cost. (integer, minimum 1, default 3)
  -f <offset> / --qualityoffset <offset>: Set the ascii offset value in fastq
      files. If not specified, the offset is estimated by examining the input files.
  -a / --autoadapter: When the fragment being sequenced is shorter than the
      individual reads, the ends of the reads contain adapter sequence. With this
      option, such adapters are automatically removed.