kallisto command not found

Introduction

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

kallisto: command not found

or when using sudo you get the following error message

sudo: kallisto: command not found

Solutions to kallisto: command not found

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

In Ubuntu kallisto is provided by kallisto package.

kallisto is:

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.

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

sudo apt-get -y install kallisto

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

You can also use apt command to install kallisto.

sudo apt -y install kallisto

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

sudo aptitude install kallisto

Summary

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