How To Install pbdagcon on Debian 9
Introduction
In this tutorial we learn how to install pbdagcon on Debian 9.
What is pbdagcon
pbdagcon is:
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.
It uses the alignment information from blasr to align sequence reads to a “backbone” sequence. Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the “backbone” sequences. A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus. The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality.
While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose. Currently, it only takes FASTA input. For shorter read sequences, one might need to adjust the blasr alignment parameters to get the alignment string properly.
The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads and pre-assembly.
There are three methods to install pbdagcon 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 pbdagcon Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pbdagcon using apt-get by running the following command:
sudo apt-get -y install pbdagcon
Install pbdagcon Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pbdagcon using apt by running the following command:
sudo apt -y install pbdagcon
Install pbdagcon 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 pbdagcon using aptitude by running the following command:
sudo aptitude -y install pbdagcon
How To Uninstall pbdagcon on Debian 9
To uninstall only the pbdagcon package we can use the following command:
sudo apt-get remove pbdagcon
Uninstall pbdagcon And Its Dependencies
To uninstall pbdagcon and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove pbdagcon
Remove pbdagcon Configurations and Data
To remove pbdagcon configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge pbdagcon
Remove pbdagcon configuration, data, and all of its dependencies
We can use the following command to remove pbdagcon configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pbdagcon
Dependencies
pbdagcon have the following dependencies:
References
Summary
In this tutorial we learn how to install pbdagcon package on Debian 9 using different package management tools: apt, apt-get and aptitude.