How To Install r-bioc-dada2 on Kali Linux

In this tutorial we learn how to install r-bioc-dada2 on Kali Linux. r-bioc-dada2 is sample inference from amplicon sequencing data

Introduction

In this tutorial we learn how to install r-bioc-dada2 on Kali Linux.

What is r-bioc-dada2

r-bioc-dada2 is:

The dada2 package contributes to software workflows to interpret sequencing data from microbiota - the relative abundance of bacterial and/or yeast, typically measured in the gut. It infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

There are three methods to install r-bioc-dada2 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 r-bioc-dada2 Using apt-get

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

sudo apt-get update

After updating apt database, We can install r-bioc-dada2 using apt-get by running the following command:

sudo apt-get -y install r-bioc-dada2

Install r-bioc-dada2 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install r-bioc-dada2 using apt by running the following command:

sudo apt -y install r-bioc-dada2

Install r-bioc-dada2 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 r-bioc-dada2 using aptitude by running the following command:

sudo aptitude -y install r-bioc-dada2

How To Uninstall r-bioc-dada2 on Kali Linux

To uninstall only the r-bioc-dada2 package we can use the following command:

sudo apt-get remove r-bioc-dada2

Uninstall r-bioc-dada2 And Its Dependencies

To uninstall r-bioc-dada2 and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove r-bioc-dada2

Remove r-bioc-dada2 Configurations and Data

To remove r-bioc-dada2 configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge r-bioc-dada2

Remove r-bioc-dada2 configuration, data, and all of its dependencies

We can use the following command to remove r-bioc-dada2 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge r-bioc-dada2

Dependencies

r-bioc-dada2 have the following dependencies:

References

Summary

In this tutorial we learn how to install r-bioc-dada2 package on Kali Linux using different package management tools: apt, apt-get and aptitude.