How To Install ivar-doc on Kali Linux

In this tutorial we learn how to install ivar-doc on Kali Linux. ivar-doc is functions broadly useful for viral amplicon-based sequencing (documentation)

Introduction

In this tutorial we learn how to install ivar-doc on Kali Linux.

What is ivar-doc

ivar-doc is:

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. iVar provided the following functions:

  1. trimming of primers and low-quality bases,
  2. consensus calling,
  3. variant calling - both iSNVs and insertions/deletions, and
  4. identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.

This package contains the html documentation for ivar.

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

Install ivar-doc Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install ivar-doc

Install ivar-doc Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install ivar-doc

Install ivar-doc Using aptitude

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

sudo aptitude update

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

sudo aptitude -y install ivar-doc

How To Uninstall ivar-doc on Kali Linux

To uninstall only the ivar-doc package we can use the following command:

sudo apt-get remove ivar-doc

Uninstall ivar-doc And Its Dependencies

To uninstall ivar-doc and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove ivar-doc

Remove ivar-doc Configurations and Data

To remove ivar-doc configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge ivar-doc

Remove ivar-doc configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge ivar-doc

Dependencies

ivar-doc have the following dependencies:

References

Summary

In this tutorial we learn how to install ivar-doc package on Kali Linux using different package management tools: apt, apt-get and aptitude.