simple − the obvious array-based kmer counter
simple [−f|−r|−C] [−c compression] [−m mersize] −i input −o output
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.
−i input
−o output
−m mersize
the mer size. Default is 22
−f |
forward kmer (this is the default) |
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−r |
reverse kmer |
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−C |
canonical kmer (lexicographically smaller of the forward and reverse kmer at each location) |
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−c # |
mer compression |