kmc command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

kmc: command not found

or when using sudo you get the following error message

sudo: kmc: command not found

Solutions to kmc: command not found

How To Fix kmc: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu kmc is provided by kmc package.

kmc is:

The kmc software is designed for counting k-mers (sequences of consecutive k symbols) in a set of reads. K-mer counting is important for many bioinformatics applications, e.g. developing de Bruijn graph assemblers.

Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencing. Unfortunately, sequencing errors (frequent in practice) result in huge memory requirements for de Bruijn graphs, as well as long build time. One of the popular approaches to handle this problem is filtering the input reads in such a way that unique k-mers (very likely obtained as a result of an error) are discarded.

Thus, KMC scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented in KMC makes use mostly of disk space rather than RAM, which allows one to use KMC even on rather typical personal computers. When run on high-end servers (what is necessary for KMC competitors) it outperforms them in both memory requirements and speed of computation. The disk space necessary for computation is in order of the size of input data (usually it is smaller).

To fix this problem, we can install more using the command below.

sudo apt-get -y install kmc

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install kmc.

sudo apt -y install kmc

Or if you have aptitude installed you can use the following command.

sudo aptitude install kmc

Summary

In this tutorial we learn how to fix kmc command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.