How To Install wtdbg2 on Debian 11
Introduction
In this tutorial we learn how to install wtdbg2 on Debian 11.
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 Debian 11. 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 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 wtdbg2 using aptitude by running the following command:
sudo aptitude -y install wtdbg2
How To Uninstall wtdbg2 on Debian 11
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 Debian 11, we can use the command below:
sudo apt-get -y autoremove wtdbg2
Remove wtdbg2 Configurations and Data
To remove wtdbg2 configuration and data from Debian 11 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:
References
Summary
In this tutorial we learn how to install wtdbg2 package on Debian 11 using different package management tools: apt, apt-get and aptitude.