Introduction
In this tutorial we learn how to install atropos on Kali Linux.
What is atropos
atropos is:
Atropos is tool for specific, sensitive, and speedy trimming of NGS
reads. It is a fork of the venerable Cutadapt read trimmer, with the
primary improvements being:
- Multi-threading support, including an extremely fast “parallel
write” mode. - Implementation of a new insert alignment-based trimming algorithm
for paired-end reads that is substantially more sensitive and
specific than the original Cutadapt adapter alignment-based
algorithm. This algorithm can also correct mismatches between the
overlapping portions of the reads. - Options for trimming specific types of data (miRNA, bisulfite-seq).
- A new command (‘detect’) that will detect adapter sequences and
other potential contaminants. - A new command (’error’) that will estimate the sequencing error
rate, which helps to select the appropriate adapter- and quality-
trimming parameter values. - A new command (‘qc’) that generates read statistics similar to
FastQC. The trim command can also compute read statistics both
before and after trimming (using the ‘–stats’ option). - Improved summary reports, including support for serialization
formats (JSON, YAML, pickle), support for user-defined templates
(via the optional Jinja2 dependency), and integration with MultiQC. - The ability to merge overlapping reads (this is experimental and
the functionality is limited). - The ability to write the summary report and log messages to
separate files. - The ability to read SAM/BAM files and read/write interleaved
FASTQ files. - Direct trimming of reads from an SRA accession.
- A progress bar, and other minor usability enhancements.
There are three methods to install atropos 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 atropos Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install atropos using apt-get by running the following command:
sudo apt-get -y install atroposInstall atropos Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install atropos using apt by running the following command:
sudo apt -y install atroposInstall atropos 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 updateAfter updating apt database, We can install atropos using aptitude by running the following command:
sudo aptitude -y install atropos
How To Uninstall atropos on Kali Linux
To uninstall only the atropos package we can use the following command:
sudo apt-get remove atropos
Uninstall atropos And Its Dependencies
To uninstall atropos and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove atropos
Remove atropos Configurations and Data
To remove atropos configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge atropos
Remove atropos configuration, data, and all of its dependencies
We can use the following command to remove atropos configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge atropos
Dependencies
atropos have the following dependencies:
References
Summary
In this tutorial we learn how to install atropos package on Kali Linux using different package management tools: apt, apt-get and aptitude.
