NAME

       wham-build - Wisconsin's High-Throughput Alignment Method

DESCRIPTION

   Usage:
              wham-build  [options]*  -l <int> <ref_sequence> <basepath> -l <int>         specify
              the length of short reads <ref_sequence>   comma-separated list of fiels  with  ref
              sequences <basepath>       write wham data to files with this dir/basename

OPTIONS

       -v <int>
              report hits with <=v errors (0-5), ignore qualities

       -p <int>
              specify the number of fragments for alignments

       -m <int>
              discard subsequences appearing more than <int> times (default: 100).

       -b <int>
              specify the number of buckets

       -a     find all valid matches (need much more memory)

       --mask keep masked characters in the sequences (default: on)

       --unmask
              discard masked characters in the sequences. Masks are treated as Ns

       --version
              print version information

       -h/--help
              print this usage message

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.