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)