.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KMC "1" "November 2018" "K-Mer Counter (KMC) ver. 2.3.0 (2015-08-21)" "kmc"
.SH NAME
kmc - count kmers in genomic sequences
.SH 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.

.SH SYNOPSIS
kmc [options] <input_file_name> <output_file_name> <working_directory>
.PP
kmc [options] <@input_file_names> <output_file_name> <working_directory>
.SH OPTIONS
.HP
\fB\-v\fR \- verbose mode (shows all parameter settings); default: false
.HP
\fB\-k\fR<len> \- k\-mer length (k from 1 to 256; default: 25)
.HP
\fB\-m\fR<size> \- max amount of RAM in GB (from 1 to 1024); default: 12
.HP
\fB\-sm\fR \- use strict memory mode (memory limit from \fB\-m\fR<n> switch will not be exceeded)
.HP
\fB\-p\fR<par> \- signature length (5, 6, 7, 8); default: 7
.HP
\fB\-f\fR<a/q/m> \- input in FASTA format (\fB\-fa\fR), FASTQ format (\fB\-fq\fR) or mulit FASTA (\fB\-fm\fR); default: FASTQ
.HP
\fB\-q[value]\fR \- use Quake's compatible counting with [value] representing lowest quality (default: 33)
.HP
\fB\-ci\fR<value> \- exclude k\-mers occurring less than <value> times (default: 2)
.HP
\fB\-cs\fR<value> \- maximal value of a counter (default: 255)
.HP
\fB\-cx\fR<value> \- exclude k\-mers occurring more of than <value> times (default: 1e9)
.HP
\fB\-b\fR \- turn off transformation of k\-mers into canonical form
.HP
\fB\-r\fR \- turn on RAM\-only mode
.HP
\fB\-n\fR<value> \- number of bins
.HP
\fB\-t\fR<value> \- total number of threads (default: no. of CPU cores)
.HP
\fB\-sf\fR<value> \- number of FASTQ reading threads
.HP
\fB\-sp\fR<value> \- number of splitting threads
.HP
\fB\-sr\fR<value> \- number of sorter threads
.HP
\fB\-so\fR<value> \- number of threads per single sorter
.PP
.SH EXAMPLES
kmc \fB\-k27\fR \fB\-m24\fR NA19238.fastq NA.res \edata\ekmc_tmp_dir\e
.PP
kmc \fB\-k27\fR \fB\-q\fR \fB\-m24\fR @files.lst NA.res \edata\ekmc_tmp_dir\e
.SH "AUTHOR"
.sp
kmc was originally written by:
.PP
Sebastian Deorowicz (sebastian.deorowicz@polsl.pl)
.PP
Marek Kokot
.PP
Szymon Grabowski
.PP
Agnieszka Debudaj-Grabysz

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