atropos command not found

In this troubleshooting guide we learn how to fix atropos command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

atropos: command not found

or when using sudo you get the following error message

sudo: atropos: command not found

Solutions to atropos: command not found

How To Fix atropos: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu atropos is provided by atropos package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install atropos

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install atropos.

sudo apt -y install atropos

Or if you have aptitude installed you can use the following command.

sudo aptitude install atropos

Summary

In this tutorial we learn how to fix atropos command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.