sort_reads command not found

Introduction

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

sort_reads: command not found

or when using sudo you get the following error message

sudo: sort_reads: command not found

Solutions to sort_reads: command not found

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

In Ubuntu sort_reads is provided by idba-extra package.

idba-extra is:

IDBA stands for iterative de Bruijn graph assembler. In computational sequence biology, an assembler solves the puzzle coming from large sequencing machines that feature many gigabytes of short reads from a large genome.

This package provides several flavours of the IDBA assembler, as they all share the same source tree but serve different purposes and evolved over time.

IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.

This package ships extra tools for using idba in specific situations.

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

sudo apt-get -y install idba-extra

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

You can also use apt command to install idba-extra.

sudo apt -y install idba-extra

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

sudo aptitude install idba-extra

Summary

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