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:
References
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
.