---
name: "kmc_tools-intersect"
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-intersect"
---

# kmc\_tools-intersect(1)

calculate intersection of two KMC databases

## NAME

kmc\_tools-intersect - calculate intersection of two KMC databases

## SYNOPSIS

**kmc\_tools intersect** \<input1 \[input1\_params\]\> \<input2 \[input2\_params\]\> \<output \[output\_params\]\>

## DESCRIPTION

The output database will contain only k-mers that are present in both input sets. The counter value in the output database is equal to the lower counter value in the input.

## OPTIONS

For each input 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 output 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

**-cs\<value\>**

maximal value of a counter

## EXAMPLE

```
kmc -k28 file1.fastq kmers1 tmp
kmc -k28 file2.fastq kmers2 tmp
kmc_tools intersect kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 kmers1_kmers2_intersect -ci20 -cx150
```

## 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.