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.