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KMC(1) kmc KMC(1)


K-Mer Counter (KMC) ver. 2.3.0 - kmc


KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.


kmc [options] <input_file_name> <output_file_name> <working_directory>

kmc [options] <@input_file_names> <output_file_name> <working_directory>


-v - verbose mode (shows all parameter settings); default: false

-k<len> - k-mer length (k from 1 to 256; default: 25)

-m<size> - max amount of RAM in GB (from 1 to 1024); default: 12

-sm - use strict memory mode (memory limit from -m<n> switch will not be exceeded)

-p<par> - signature length (5, 6, 7, 8); default: 7

-f<a/q/m> - input in FASTA format (-fa), FASTQ format (-fq) or mulit FASTA (-fm); default: FASTQ

-q[value] - use Quake's compatible counting with [value] representing lowest quality (default: 33)

-ci<value> - exclude k-mers occurring less than <value> times (default: 2)

-cs<value> - maximal value of a counter (default: 255)

-cx<value> - exclude k-mers occurring more of than <value> times (default: 1e9)

-b - turn off transformation of k-mers into canonical form

-r - turn on RAM-only mode

-n<value> - number of bins

-t<value> - total number of threads (default: no. of CPU cores)

-sf<value> - number of FASTQ reading threads

-sp<value> - number of splitting threads

-sr<value> - number of sorter threads

-so<value> - number of threads per single sorter


kmc -k27 -m24 NA19238.fastq NA.res \data\kmc_tmp_dir\

kmc -k27 -q -m24 @files.lst NA.res \data\kmc_tmp_dir\


kmc was originally written by:

Sebastian Deorowicz (

Marek Kokot

Szymon Grabowski

Agnieszka Debudaj-Grabysz


KMC is a free software distributed under GNU GPL3 licence for academic, research, and commercial use.

April 2020 K-Mer (2015-08-21)