simple1
The obvious array-based kmer counter
Usage
simple [{-f | -r | -C}]
[-c
compression]
[-m
mersize]
-i
input
-o
output
Overview
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
-iinput
-ooutput
-mmersize-
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
Releases
6 releases since Debian 6.0 (Squeeze); the text changed 1 time.
-C since Debian 9 (Stretch);
-f since Debian 9 (Stretch);
-r since Debian 9 (Stretch).