skewer command not found

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

Introduction

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

skewer: command not found

or when using sudo you get the following error message

sudo: skewer: command not found

Solutions to skewer: command not found

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

In Ubuntu skewer is provided by skewer package.

skewer is:

skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

Features

  • Detection and removal of adapter sequences
  • Insertion and deletion allowed in pattern matching
  • Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads
  • Demultiplexing of barcoded sequencing runs
  • Multi-threading support
  • Trimming based on phred quality scores
  • IUPAC characters for barcodes and adapters
  • Compressed input and output support

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

sudo apt-get -y install skewer

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

You can also use apt command to install skewer.

sudo apt -y install skewer

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

sudo aptitude install skewer

Summary

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