jellyfish command not found

Introduction

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

jellyfish: command not found

or when using sudo you get the following error message

sudo: jellyfish: command not found

Solutions to jellyfish: command not found

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

In Ubuntu jellyfish is provided by jellyfish package.

jellyfish is:

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.

JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the “jellyfish dump” command.

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

sudo apt-get -y install jellyfish

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

You can also use apt command to install jellyfish.

sudo apt -y install jellyfish

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

sudo aptitude install jellyfish

Summary

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