How To Install python3-pairtools on Kali Linux

In this tutorial we learn how to install python3-pairtools on Kali Linux. python3-pairtools is Framework to process sequencing data from a Hi-C experiment

Introduction

In this tutorial we learn how to install python3-pairtools on Kali Linux.

What is python3-pairtools

python3-pairtools is:

Simple and fast command-line framework to process sequencing data from a Hi-C experiment.

Process pair-end sequence alignments and perform the following operations:

  • Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules
  • Sort .pairs files for downstream analyses
  • Detect, tag and remove PCR/optical duplicates
  • Generate extensive statistics of Hi-C datasets
  • Select Hi-C pairs given flexibly defined criteria
  • Restore .sam alignments from Hi-C pairs

There are three methods to install python3-pairtools 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 python3-pairtools Using apt-get

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

sudo apt-get update

After updating apt database, We can install python3-pairtools using apt-get by running the following command:

sudo apt-get -y install python3-pairtools

Install python3-pairtools Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-pairtools using apt by running the following command:

sudo apt -y install python3-pairtools

Install python3-pairtools 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 python3-pairtools using aptitude by running the following command:

sudo aptitude -y install python3-pairtools

How To Uninstall python3-pairtools on Kali Linux

To uninstall only the python3-pairtools package we can use the following command:

sudo apt-get remove python3-pairtools

Uninstall python3-pairtools And Its Dependencies

To uninstall python3-pairtools and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove python3-pairtools

Remove python3-pairtools Configurations and Data

To remove python3-pairtools configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge python3-pairtools

Remove python3-pairtools configuration, data, and all of its dependencies

We can use the following command to remove python3-pairtools configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-pairtools

Dependencies

python3-pairtools have the following dependencies:

References

Summary

In this tutorial we learn how to install python3-pairtools package on Kali Linux using different package management tools: apt, apt-get and aptitude.