salmon command not found

Introduction

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

salmon: command not found

or when using sudo you get the following error message

sudo: salmon: command not found

Solutions to salmon: command not found

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

In Ubuntu salmon is provided by salmon package.

salmon is:

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many different pipelines. For example, you can choose to make use of the lightweight alignments by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. computed with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment.

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

sudo apt-get -y install salmon

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

You can also use apt command to install salmon.

sudo apt -y install salmon

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

sudo aptitude install salmon

Summary

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