TrimmomaticPE command not found

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

Introduction

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

TrimmomaticPE: command not found

or when using sudo you get the following error message

sudo: TrimmomaticPE: command not found

Solutions to TrimmomaticPE: command not found

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

In Ubuntu TrimmomaticPE is provided by trimmomatic package.

trimmomatic is:

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

The current trimming steps are:

  • ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
  • SLIDINGWINDOW: Perform a sliding window trimming, cutting once thes average quality within the window falls below a threshold.
  • LEADING: Cut bases off the start of a read, if below a threshold quality
  • TRAILING: Cut bases off the end of a read, if below a threshold quality
  • CROP: Cut the read to a specified length
  • HEADCROP: Cut the specified number of bases from the start of the read
  • MINLENGTH: Drop the read if it is below a specified length
  • TOPHRED33: Convert quality scores to Phred-33
  • TOPHRED64: Convert quality scores to Phred-64 It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp’ed FASTQ. Use of gzip format is determined based on the .gz extension.

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

sudo apt-get -y install trimmomatic

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

You can also use apt command to install trimmomatic.

sudo apt -y install trimmomatic

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

sudo aptitude install trimmomatic

Summary

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