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