NAME

       simple - the obvious array-based kmer counter

SYNOPSIS

       simple [-f|-r|-C] [-c compression] [-m mersize] -i input -o output

DESCRIPTION

       simple  is a very simple mer counter.  It allocates a gigantic 32-bit array, populates the
       array with mers, sorts, and writes the output.  It will allocate 4 bytes per  kmer.   k=16
       will require 16 GB to run.

OPTIONS

       -i input

       -o output

       -m mersize
              the mer size.  Default is 22

       -f     forward kmer (this is the default)

       -r     reverse kmer

       -C     canonical  kmer  (lexicographically smaller of the forward and reverse kmer at each
              location)

       -c #   mer compression

SEE ALSO

       meryl(1)