NAME

       kmc - 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)

       -hc - count homopolymer compressed k-mers (approximate and experimental)

       -p<par> - signature length (5, 6, 7, 8, 9, 10, 11); default: 9

       -f<a/q/m/bam/kmc> - input in FASTA format (-fa), FASTQ format (-fq), multi FASTA (-fm)  or
              BAM (-fbam) or KMC(-fkmc); default: FASTQ

       -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 threads for 2nd stage

       -j<file_name> - file name with execution summary in JSON format

       -w - without output

       -o<kmc/kff> - output in KMC of KFF format; default: KMC

       -hp - hide percentage progress (default: false)

       -e - only estimate histogram of k-mers occurrences instead of exact k-mer counting

       --opt-out-size - optimize output database size (may increase running time)

EXAMPLES

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

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

AUTHOR

       kmc was originally written by:

       Sebastian Deorowicz (sebastian.deorowicz@polsl.pl)

       Marek Kokot

       Szymon Grabowski

       Agnieszka Debudaj-Grabysz

COPYING

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