Options for clc_mapper

CLC Read Mapper
Usage information:
  -d / --references         Reference database file(s) to use.
  -z / --circular           Indicate that the following reference file contains circular sequences, eg. -d -z mito.fa.
  -n / --indexoutput        Save index to file, eg. hg19.idx.
  -q / --reads              Read file(s) to use, eg. read.fastq.
  -p / --paired             Set paired parameters, eg. fb ss 50 250.
  -i / --interleave         Form read pairs by interleaving two files, eg. -i mate1.fastq mate2.fastq.
       --type               Set technology hint to normal or pacbio (default is normal).
  -S / --normaltypelimit    Switch to long read mapping for reads beyond this length (default is 500).
  -o / --output             Resulting alignments, eg. result.cas.
  -m / --matchscore         Set match score (integer range 1 to 10, default 1).
  -x / --mismatchcost       Set mismatch cost (integer range 1 to 10, default 2).
  -g / --gapcost            Set insertion and deletion cost (integer range 1 to 3, default 3).
  -G / --gapopen            Set affine insertion and deletion open cost (integer from 0 to 10, default 0 (linear)).
  -e / --deletioncost       Set deletion cost (integer range 1 to 3, default is gapcost).
  -E / --deletionopen       Set affine deletion open cost (integer from 0 to 10, default is gapopen).
  -a / --alignmode          Set local or global alignment mode (default local).
  -f / --forwardonly        Restrict mapping to the forward strand.
  -b / --backwardonly       Restrict mapping to the backward strand.
  -r / --repeat             Report random hits for multi-hits or ignore them (default random).
  -t / --maxalign           Set the maximum number of hits to report for each read (default 1).
  -s / --similarity         Set similarity score (default 0.8).
  -l / --lengthfraction     Set length fraction (default 0.5).
       --noprogress         Hide progress indicator.
       --cpus               Restrict the number of threads to be used, eg. --cpus 20 (default unlimited).
  -M / --mappermemory       Restrict the amount of memory (MB) to use during mapping. Overrides --cpus parameter.