How To Install kaptive-example on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 552 words
Introduction
In this tutorial we learn how to install kaptive-example on Ubuntu.
What is kaptive-example
kaptive-example is:
Kaptive reports information about K and O types for Klebsiella genome assemblies.
Given a novel genome and a database of known loci (K or O), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:
- BLAST for all known locus nucleotide sequences (using blastn) to identify the best match (‘best’ defined as having the highest coverage).
- Extract the region(s) of the assembly which correspond to the BLAST hits (i.e. the locus sequence in the assembly) and save it to a FASTA file.
- BLAST for all known locus genes (using tblastn) to identify which expected genes (genes in the best matching locus) are present/missing and whether any unexpected genes (genes from other loci) are present.
- Output a summary to a table file.
In cases where your input assembly closely matches a known locus, Kaptive should make that obvious. When your assembly has a novel type, that too should be clear. However, Kaptive cannot reliably extract or annotate locus sequences for totally novel types - if it indicates a novel locus is present then extracting and annotating the sequence is up to you! Very poor assemblies can confound the results, so be sure to closely examine any case where the locus sequence in your assembly is broken into multiple pieces.
This package contains some example data.
There are three methods to install kaptive-example 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 kaptive-example Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install kaptive-example using apt-get by running the following command:
sudo apt-get -y install kaptive-example
Install kaptive-example Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install kaptive-example using apt by running the following command:
sudo apt -y install kaptive-example
Install kaptive-example 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 kaptive-example using aptitude by running the following command:
sudo aptitude -y install kaptive-example
How To Uninstall kaptive-example on Ubuntu
To uninstall only the kaptive-example package we can use the following command:
sudo apt-get remove kaptive-example
Uninstall kaptive-example And Its Dependencies
To uninstall kaptive-example and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove kaptive-example
Remove kaptive-example Configurations and Data
To remove kaptive-example configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge kaptive-example
Remove kaptive-example configuration, data, and all of its dependencies
We can use the following command to remove kaptive-example configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge kaptive-example
Dependencies
kaptive-example have the following dependencies:
References
Summary
In this tutorial we learn how to install kaptive-example package on Ubuntu using different package management tools: apt, apt-get and aptitude.