kmc(1) count kmers in genomic sequences

DESCRIPTION

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.

SYNOPSIS

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

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

OPTIONS

-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

EXAMPLES

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

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

AUTHOR

kmc was originally written by:

Sebastian Deorowicz ([email protected])

Marek Kokot

Szymon Grabowski

Agnieszka Debudaj-Grabysz

COPYING

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