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