How To Install seqsero on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 478 words
Introduction
In this tutorial we learn how to install seqsero on Ubuntu.
What is seqsero
seqsero is:
SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.
SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing
- raw reads from genomes of 308 Salmonella isolates of known serotype
- raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and
- 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.
There are three methods to install seqsero on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install seqsero Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install seqsero using apt-get by running the following command:
sudo apt-get -y install seqsero
Install seqsero Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install seqsero using apt by running the following command:
sudo apt -y install seqsero
Install seqsero 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install seqsero using aptitude by running the following command:
sudo aptitude -y install seqsero
How To Uninstall seqsero on Ubuntu
To uninstall only the seqsero package we can use the following command:
sudo apt-get remove seqsero
Uninstall seqsero And Its Dependencies
To uninstall seqsero and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove seqsero
Remove seqsero Configurations and Data
To remove seqsero configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge seqsero
Remove seqsero configuration, data, and all of its dependencies
We can use the following command to remove seqsero configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge seqsero
Dependencies
seqsero have the following dependencies:
References
Summary
In this tutorial we learn how to install seqsero package on Ubuntu using different package management tools: apt, apt-get and aptitude.