How To Install wtdbg2 on Kali Linux

Introduction

In this tutorial we learn how to install wtdbg2 on Kali Linux.

What is wtdbg2

wtdbg2 is:

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.

During assembly, wtdbg2 chops reads into 1024bp segments, merges similar segments into a vertex and connects vertices based on the segment adjacency on reads. The resulting graph is called fuzzy Bruijn graph (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and keeps read paths when collapsing k-mers. The use of FBG distinguishes wtdbg2 from the majority of long-read assemblers.

There are three methods to install wtdbg2 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 wtdbg2 Using apt-get

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

sudo apt-get update

After updating apt database, We can install wtdbg2 using apt-get by running the following command:

sudo apt-get -y install wtdbg2

Install wtdbg2 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install wtdbg2 using apt by running the following command:

sudo apt -y install wtdbg2

Install wtdbg2 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 wtdbg2 using aptitude by running the following command:

sudo aptitude -y install wtdbg2

How To Uninstall wtdbg2 on Kali Linux

To uninstall only the wtdbg2 package we can use the following command:

sudo apt-get remove wtdbg2

Uninstall wtdbg2 And Its Dependencies

To uninstall wtdbg2 and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove wtdbg2

Remove wtdbg2 Configurations and Data

To remove wtdbg2 configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge wtdbg2

Remove wtdbg2 configuration, data, and all of its dependencies

We can use the following command to remove wtdbg2 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge wtdbg2

Dependencies

wtdbg2 have the following dependencies:

• libc6
• zlib1g

References

• wtdbg2 website

Summary

In this tutorial we learn how to install wtdbg2 package on Kali Linux using different package management tools: apt, apt-get and aptitude.