NAME

       kmc_tools-filter - filter out reads with too small number of k-mers

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 (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.

                                                                              KMC_TOOLS-FILTER(1)