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SIMPLE(1) |
User Commands |
SIMPLE(1) |
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