Options (default values):

  -a  N  specify band expansion size N > 10 (20)
  -b  N  specify base quality cutoff for differences N > 15 (20)
  -c  N  specify base quality cutoff for clipping N > 5 (12)
  -d  N  specify max qscore sum at differences N > 100 (200)
  -e  N  specify extra number of differences N > 10 (20)
  -f  N  specify max gap length in any overlap N > 10 (300)
  -g  N  specify gap penalty factor N > 0 (6)
  -h  N  specify max overhang percent length N > 5 (20)
  -i  N  specify segment pair score cutoff N > 20 (40)
  -j  N  specify chain score cutoff N > 30 (80)
  -k  N  specify end clipping flag N >= 0 (1)
  -m  N  specify match score factor N > 0 (2)
  -n  N  specify mismatch score factor N < 0 (-5)
  -o  N  specify overlap length cutoff > 15 (40)
  -p  N  specify overlap percent identity cutoff N > 65 (90)
  -r  N  specify reverse orientation value N >= 0 (1)
  -s  N  specify overlap similarity score cutoff N > 250 (900)
  -t  N  specify max number of word occurrences N > 30 (500)
  -u  N  specify min number of constraints for correction N > 0 (4)
  -v  N  specify min number of constraints for linking N > 0 (2)
  -w  N  specify file name for clipping information (none)
  -x  N  specify prefix string for output file names (cap)
  -y  N  specify clipping range N > 5 (100)
  -z  N  specify min no. of good reads at clip pos N > 0 (2)