sickle command not found

Introduction

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

sickle: command not found

or when using sudo you get the following error message

sudo: sickle: command not found

Solutions to sickle: command not found

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

In Ubuntu sickle is provided by sickle package.

sickle is:

Most modern sequencing technologies produce reads that have deteriorating quality towards the 3’-end. Incorrectly called bases here negatively impact assembles, mapping, and downstream bioinformatics analyses.

Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3’-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window drops below the threshold. At that point the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there. However, if the cut point is less than the minimum length threshold, then the read is discarded entirely.

Sickle supports four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close.

Sickle also supports gzipped file inputs.

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

sudo apt-get -y install sickle

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

You can also use apt command to install sickle.

sudo apt -y install sickle

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

sudo aptitude install sickle

Summary

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