How To Install dascrubber on Debian 10

In this tutorial we learn how to install dascrubber on Debian 10. dascrubber is alignment-based scrubbing pipeline for DNA sequencing reads

Introduction

In this tutorial we learn how to install dascrubber on Debian 10.

What is dascrubber

The Dazzler Scrubbing Suite produces a set of edited reads that are guaranteed to

  • be continuous stretches of the underlying genome (i.e. no unremoved adapters and not chimers)
  • have no very low quality stretches (i.e. the error rate never exceeds some reasonable maximum, 20% or so in the case of Pacbio data). Its secondary goal is to do so with the minimum removal of data and splitting of reads.

There are three ways to install dascrubber on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install dascrubber Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install dascrubber

Install dascrubber Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install dascrubber

Install dascrubber 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 dascrubber using aptitude by running the following command:

sudo aptitude -y install dascrubber

How To Uninstall dascrubber on Debian 10

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

sudo apt-get remove dascrubber

Uninstall dascrubber And Its Dependencies

To uninstall dascrubber and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove dascrubber

Remove dascrubber Configurations and Data

To remove dascrubber configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge dascrubber

Remove dascrubber configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge dascrubber

References

Summary

In this tutorial we learn how to install dascrubber on Debian 10 using different package management tools like apt, apt-get and aptitude.