shasta command not found

Introduction

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

shasta: command not found

or when using sudo you get the following error message

sudo: shasta: command not found

Solutions to shasta: command not found

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

In Ubuntu shasta is provided by shasta package.

shasta is:

De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

• Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.

• Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers.

This package contains the executable binaries (tools) and accommodating scripts.

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

sudo apt-get -y install shasta

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

You can also use apt command to install shasta.

sudo apt -y install shasta

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

sudo aptitude install shasta

Summary

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