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 |