How To Install segemehl on Debian 12
Introduction
In this tutorial we learn how to install segemehl on Debian 12.
What is segemehl
segemehl is:
Segemehl is a software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed and bgzip’ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file. In the case of split-read mapping, additional BED files are written to the disc. These BED files may be summarized with the postprocessing tool haarz. In the case of the alignment of bisulfite converted reads, raw methylation rates may also be called with haarz.
In brief, for each suffix of a read, segemehl aims to find the best-scoring seed. Seeds might contain insertions, deletions, and mismatches (differences). The number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program. Subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. Finally, reads with a minimum accuracy of percent are reported to the user.
There are three methods to install segemehl on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install segemehl Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install segemehl using apt-get by running the following command:
sudo apt-get -y install segemehl
Install segemehl Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install segemehl using apt by running the following command:
sudo apt -y install segemehl
Install segemehl 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 segemehl using aptitude by running the following command:
sudo aptitude -y install segemehl
How To Uninstall segemehl on Debian 12
To uninstall only the segemehl package we can use the following command:
sudo apt-get remove segemehl
Uninstall segemehl And Its Dependencies
To uninstall segemehl and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove segemehl
Remove segemehl Configurations and Data
To remove segemehl configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge segemehl
Remove segemehl configuration, data, and all of its dependencies
We can use the following command to remove segemehl configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge segemehl
Dependencies
segemehl have the following dependencies:
References
Summary
In this tutorial we learn how to install segemehl package on Debian 12 using different package management tools: apt, apt-get and aptitude.
