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SIMPLE

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

SEE ALSO

meryl(1)

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