How To Install mira-assembler on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 472 words

Introduction

In this tutorial we learn how to install mira-assembler on Ubuntu.

What is `mira-assembler`

mira-assembler is:

The mira genome fragment assembler is a specialised assembler for sequencing projects classified as ‘hard’ due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occurring in different variations thereof.

The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.

The package provides the following executables: Binaries provided:

mira: for assembly of genome sequences
miramem: estimating memory needed to assemble projects.
mirabait: a “grep” like tool to select reads with kmers up to 256 bases.
miraconvert: is a tool to convert, extract and sometimes recalculate all kinds of data related to sequence assembly files.

There are three methods to install mira-assembler on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install mira-assembler Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install mira-assembler using apt-get by running the following command:

sudo apt-get -y install mira-assembler

Install mira-assembler Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install mira-assembler using apt by running the following command:

sudo apt -y install mira-assembler

Install mira-assembler Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install mira-assembler using aptitude by running the following command:

sudo aptitude -y install mira-assembler

How To Uninstall mira-assembler on Ubuntu

To uninstall only the mira-assembler package we can use the following command:

sudo apt-get remove mira-assembler

Uninstall mira-assembler And Its Dependencies

To uninstall mira-assembler and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove mira-assembler

Remove mira-assembler Configurations and Data

To remove mira-assembler configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge mira-assembler

Remove mira-assembler configuration, data, and all of its dependencies

We can use the following command to remove mira-assembler configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge mira-assembler

Dependencies

mira-assembler have the following dependencies:

References

mira-assembler website

Summary

In this tutorial we learn how to install mira-assembler package on Ubuntu using different package management tools: apt, apt-get and aptitude.