simple - Online in the Cloud

PROGRAM:

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

Use simple online using onworks.net services