How To Install spades on Debian 12
Introduction
In this tutorial we learn how to install spades on Debian 12.
What is spades
spades is:
The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads.
This package provides the following additional pipelines:
- metaSPAdes ?? a pipeline for metagenomic data sets
- plasmidSPAdes ?? a pipeline for extracting and assembling plasmids from WGS data sets
- metaplasmidSPAdes ?? a pipeline for extracting and assembling plasmids from metagenomic data sets
- rnaSPAdes ?? a de novo transcriptome assembler from RNA-Seq data
- truSPAdes ?? a module for TruSeq barcode assembly
- biosyntheticSPAdes ?? a module for biosynthetic gene cluster assembly with paired-end reads
SPAdes provides several stand-alone binaries with relatively simple command-line interface: k-mer counting (spades-kmercounter), assembly graph construction (spades-gbuilder) and long read to graph aligner (spades-gmapper).
There are three methods to install spades 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 spades Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install spades using apt-get by running the following command:
sudo apt-get -y install spades
Install spades Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install spades using apt by running the following command:
sudo apt -y install spades
Install spades 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 spades using aptitude by running the following command:
sudo aptitude -y install spades
How To Uninstall spades on Debian 12
To uninstall only the spades package we can use the following command:
sudo apt-get remove spades
Uninstall spades And Its Dependencies
To uninstall spades and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove spades
Remove spades Configurations and Data
To remove spades configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge spades
Remove spades configuration, data, and all of its dependencies
We can use the following command to remove spades configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge spades
Dependencies
spades have the following dependencies:
References
Summary
In this tutorial we learn how to install spades package on Debian 12 using different package management tools: apt, apt-get and aptitude.
