simple(1) the obvious array-based kmer counter


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


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.


-i input
-o output
-m mersize
the mer size. Default is 22
forward kmer (this is the default)
reverse kmer
canonical kmer (lexicographically smaller of the forward and reverse kmer at each location)
-c #
mer compression