CAP3 man page

Usage: cap3 File_of_reads [options]
File_of_reads is a file of DNA reads in FASTA formatIf the file of reads is named 'xyz', then
the file of quality values must be named 'xyz.qual',and the file of constraints named 'xyz.con'.
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 (10)
  -d  N  specify max qscore sum at differences N > 100 (200)
  -e  N  specify clearance between no. of diff N > 10 (30)
  -f  N  specify max sum of clipped quality values N >= 0 (3000)
  -g  N  specify gap penalty factor N > 0 (6)
  -m  N  specify match score factor N > 0 (2)
  -n  N  specify mismatch score factor N < 0 (-5)
  -o  N  specify overlap length cutoff > 20 (30)
  -p  N  specify overlap percent identity cutoff N > 65 (75)
  -s  N  specify overlap similarity score cutoff N > 100 (500)
  -u  N  specify min number of constraints for correction N > 0 (3)
  -v  N  specify min number of constraints for linking N > 0 (2)
  -x  N  specify prefix string for output file names (cap)