kissnp2 command not found

In this troubleshooting guide we learn how to fix kissnp2 command not found error message

Introduction

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

kissnp2: command not found

or when using sudo you get the following error message

sudo: kissnp2: command not found

Solutions to kissnp2: command not found

How To Fix kissnp2: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu kissnp2 is provided by discosnp package.

discosnp is:

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.

The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP:

  1. its mean read coverage
  2. the (phred) quality of reads generating the polymorphism.

This program is superseded by DiscoSnp++.

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

sudo apt-get -y install discosnp

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

You can also use apt command to install discosnp.

sudo apt -y install discosnp

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

sudo aptitude install discosnp

Summary

In this tutorial we learn how to fix kissnp2 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.