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