How To Install atropos on Ubuntu 22.04

In this tutorial we learn how to install atropos on Ubuntu 22.04. atropos is NGS read trimming tool that is specific, sensitive, and speedy

Introduction

In this tutorial we learn how to install atropos on Ubuntu 22.04.

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:

  1. Multi-threading support, including an extremely fast “parallel write” mode.
  2. 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.
  3. Options for trimming specific types of data (miRNA, bisulfite-seq).
  4. A new command (‘detect’) that will detect adapter sequences and other potential contaminants.
  5. A new command (’error’) that will estimate the sequencing error rate, which helps to select the appropriate adapter- and quality- trimming parameter values.
  6. 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).
  7. 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.
  8. The ability to merge overlapping reads (this is experimental and the functionality is limited).
  9. The ability to write the summary report and log messages to separate files.
  10. The ability to read SAM/BAM files and read/write interleaved FASTQ files.
  11. Direct trimming of reads from an SRA accession.
  12. A progress bar, and other minor usability enhancements.

There are three methods to install atropos 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 atropos Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install atropos using apt-get by running the following command:

sudo apt-get -y install atropos

Install 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 atropos

Install atropos 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 atropos using aptitude by running the following command:

sudo aptitude -y install atropos

How To Uninstall atropos on Ubuntu 22.04

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 Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove atropos

Remove atropos Configurations and Data

To remove atropos configuration and data from Ubuntu 22.04 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

References

Summary

In this tutorial we learn how to install atropos package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.