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.