NAME

       wham - Wisconsin's High-Throughput Alignment Method

DESCRIPTION

   Usage:
              wham  [options]*  {<readfile>  |  -1  <m1file>  -2  <m2file>}  <basepath>  <output>
              <readfile>         comma-separated list of files containing unpaired reads <m1file>
              comma-separated    list    of    files    containing    upstream   mates   <m2file>
              comma-separated list of files containing downstream mates <basepath>          write
              wham  data  to  files  with  this  dir/basename  <output>            file  to write
              alignments to

   Input options:
       -l <int>
              use first <int> bases in each read

   Alignment options:
       -v <int>
              specify the max number of errors in a reported alignment.

       -g/--gap <int>
              specify the max number of gaps in a reported alignment.

       -e/--maqerr <int>
              max sum of mismatch quals across alignment

       --nofw/--norc
              do not align to forward/reverse-complement ref strand

       --nofr/--norf
              do not align to mate1/mate2 strand: fw/rev, rev/fw.

       -I/--minins <int>
              minimum insert size for paired-end alignment (default: 0).

       -X/--maxins <int>
              maximum insert size for paired-end alignment (default: 250).

   Reporting options:
       -k <int>
              report up to <int> valid alignemtns per read (default: 1).

       -a/--all
              report all valid alignments per read.

       --best reprot valid alignments in a sorted order of quality.

       -m <int>
              discard reads with more than <int> valid alignmetns.

   Output options:
       -S/--sam
              write alignment in SAM format

       --al <fname>
              write aligned reads/pairs to file(s) <fname>

       --un <fname>
              write unaligned reads/pairs to file(s) <fname>

   Performance options:
       -t <int>
              specify the number of threads

       --nocat
              do not concatenate results from various threads

       --step <int>
              specify the number of indexes that fit into memory.

   Other options:
       --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.