SYNOPSIS

kmc_tools filter <kmc_input_db> [kmc_input_db_params] <input_read_set> [input_read_set_params] <output_read_set> [output_read_set_params]

DESCRIPTION

This command filters out reads with too small number of k-mers.

OPTIONS

For k-mers database there are additional parameters:

-ci<value>

exclude k-mers occurring less than <value> times

-cx<value>

exclude k-mers occurring more of than <value> times

For the input set of reads there are additional parameters:

-ci<value>

remove reads containing less k-mers than value. It can be integer or floating number in range [0.0;1.0]

-ci<value>

remove reads containing more k-mers than value. It can be integer or floating number in range [0.0;1.0]

-f<a/q>

input in FASTA format (-fa), FASTQ format (-fq); default: FASTQ

For the output set of reads there are additional parameters:

-f<a/q>

output in FASTA format (-fa), FASTQ format (-fq); default: same as input

EXAMPLE

kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered.fastq
kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered.fastq

AUTHOR

KMC was originally written by:

• Sebastian Deorowicz (

• Marek Kokot

• Szymon Grabowski

• Agnieszka Debudaj-Grabysz

COPYING

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