How To Install samclip on Ubuntu 22.04
Introduction
In this tutorial we learn how to install samclip
on Ubuntu 22.04.
What is samclip
samclip is:
Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in –end-to-end mode). This means the ends of the read may not be part of the best alignment.
This can be caused by:
- adapter sequences (aren’t in the reference)
- poor quality bases (mismatches only make the alignment score worse)
- structural variation in your sample compared to the reference
- reads overlapping the start and end of contigs (including circular genomes)
Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn’t. The unaligned ends of the read can be “soft” or “hard” clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don’t mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not.
There are three methods to install samclip
on Ubuntu 22.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install samclip Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install samclip
using apt-get
by running the following command:
sudo apt-get -y install samclip
Install samclip Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install samclip
using apt
by running the following command:
sudo apt -y install samclip
Install samclip 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 Ubuntu. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install samclip
using aptitude
by running the following command:
sudo aptitude -y install samclip
How To Uninstall samclip on Ubuntu 22.04
To uninstall only the samclip
package we can use the following command:
sudo apt-get remove samclip
Uninstall samclip And Its Dependencies
To uninstall samclip
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove samclip
Remove samclip Configurations and Data
To remove samclip
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge samclip
Remove samclip configuration, data, and all of its dependencies
We can use the following command to remove samclip
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge samclip
References
Summary
In this tutorial we learn how to install samclip
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.