How To Install parallel-fastq-dump on Debian 12
Introduction
In this tutorial we learn how to install parallel-fastq-dump on Debian 12.
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. 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 Debian 12. 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 first since aptitude is usually not installed by default on Debian. 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 Debian 12
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 Debian 12, 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 Debian 12 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 Debian 12 using different package management tools: apt, apt-get and aptitude.
