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= kmc_tools-filter(1)
== 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.
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