---
name: "kmc_tools-filter"
section: "1"
platform: "linux"
package: "kmc"
version: "3.2.4+dfsg-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kmc_tools-filter"
---

# kmc\_tools-filter(1)

filter out reads with too small number of k-mers

## 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.