How To Install parallel-fastq-dump on Kali Linux

Introduction

In this tutorial we learn how to install parallel-fastq-dump on Kali Linux.

What is parallel-fastq-dump

parallel-fastq-dump is:

NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing the work into multiple threads.

This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call.

There are three methods to install parallel-fastq-dump 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 parallel-fastq-dump Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install parallel-fastq-dump

Install parallel-fastq-dump Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install parallel-fastq-dump using apt by running the following command:

sudo apt -y install parallel-fastq-dump

Install parallel-fastq-dump 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 update

After updating apt database, We can install parallel-fastq-dump using aptitude by running the following command:

sudo aptitude -y install parallel-fastq-dump

How To Uninstall parallel-fastq-dump on Kali Linux

To uninstall only the parallel-fastq-dump package we can use the following command:

sudo apt-get remove parallel-fastq-dump

Uninstall parallel-fastq-dump And Its Dependencies

To uninstall parallel-fastq-dump and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove parallel-fastq-dump

Remove parallel-fastq-dump Configurations and Data

To remove parallel-fastq-dump configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge parallel-fastq-dump

Remove parallel-fastq-dump configuration, data, and all of its dependencies

We can use the following command to remove parallel-fastq-dump configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge parallel-fastq-dump

Dependencies

parallel-fastq-dump have the following dependencies:

• python3

References

• parallel-fastq-dump website

Summary

In this tutorial we learn how to install parallel-fastq-dump package on Kali Linux using different package management tools: apt, apt-get and aptitude.