How To Install pbalign on Debian 9

In this tutorial we learn how to install pbalign on Debian 9. pbalign is map Pacific Biosciences reads to reference DNA sequences

Introduction

In this tutorial we learn how to install pbalign on Debian 9.

What is pbalign

pbalign is:

pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format.

This package is part of the SMRTAnalysis suite.

There are three methods to install pbalign on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install pbalign Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install pbalign

Install pbalign Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pbalign using apt by running the following command:

sudo apt -y install pbalign

Install pbalign 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install pbalign

How To Uninstall pbalign on Debian 9

To uninstall only the pbalign package we can use the following command:

sudo apt-get remove pbalign

Uninstall pbalign And Its Dependencies

To uninstall pbalign and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove pbalign

Remove pbalign Configurations and Data

To remove pbalign configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge pbalign

Remove pbalign configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge pbalign

Dependencies

pbalign have the following dependencies:

References

Summary

In this tutorial we learn how to install pbalign package on Debian 9 using different package management tools: apt, apt-get and aptitude.