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

# kmc\_tools(1)

additional operations on k-mer databases

## NAME

kmc\_tools - additional operations on k-mer databases

## SYNOPSIS

**kmc\_tools** \[global parameters\] \<operation\> \[operation parameters\]

## DESCRIPTION

This command and its various subcomments implement a number of operations on KMC databases.

### k-mers sets operations for 2 KMC databases

**intersect**

intersection of 2 k-mers sets

**kmers\_subtract**

subtraction of 2 k-mers sets

**counters\_subtract**

counters subtraction of 2 k-mer sets

**union**

union of 2 k-mers sets

### operations for single kmc database

**sort**

sorts k-mers from database generated by KMC2.x

**reduce**

exclude too rare and too frequent k-mers

**compact**

remove counters (store only k-mers)

**histogram**

histogram of k-mers occurr ences

**dump**

dump k-mers and counters to text file

### more complex operations:

**complex**

complex operations with a number of input databases

### other operations:

**filter**

filter out reads with too small number of k-mers

## OPTIONS

### global parameters:

**-t\<value\>**

total number of threads (default: no. of CPU cores)

- **-v**

  enable verbose mode (shows some information) (default: false)

- **-hp**

  hide percentage progress (default: false)

## EXAMPLE

kmc\_tools union db1 -ci3 db2 -ci5 -cx300 db1\_union\_db2 -ci10

## SEE ALSO

[kmc(1)](/kmc/1.md), [kmc\_tools-histogram(1)](/kmc_tools-histogram/1.md), [kmc\_tools-compact(1)](/kmc_tools-compact/1.md), [kmc\_tools-intersect(1)](/kmc_tools-intersect/1.md), [kmc\_tools-complex(1)](/kmc_tools-complex/1.md), [kmc\_tools-kmers\_subtract(1)](/kmc_tools-kmers_subtract/1.md), [kmc\_tools-counters\_subtract(1)](/kmc_tools-counters_subtract/1.md), [kmc\_tools-sort(1)](/kmc_tools-sort/1.md), [kmc\_tools-dump(1)](/kmc_tools-dump/1.md), [kmc\_tools-union(1)](/kmc_tools-union/1.md), [kmc\_tools-filter(1)](/kmc_tools-filter/1.md)

## AUTHOR

KMC was originally written by:

• Sebastian Deorowicz ( \<sebastian.deorowicz@polsl.pl\>)

• Marek Kokot

• Szymon Grabowski

• Agnieszka Debudaj-Grabysz

## COPYING

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