How To Install kaptive-data on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 566 words
Introduction
In this tutorial we learn how to install kaptive-data on Ubuntu.
What is kaptive-data
kaptive-data 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 a reference database. Its not necessarily used to run kaptive since you can use your own database.
There are three methods to install kaptive-data 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-data 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-data using apt-get by running the following command:
sudo apt-get -y install kaptive-data
Install kaptive-data Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install kaptive-data using apt by running the following command:
sudo apt -y install kaptive-data
Install kaptive-data 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-data using aptitude by running the following command:
sudo aptitude -y install kaptive-data
How To Uninstall kaptive-data on Ubuntu
To uninstall only the kaptive-data package we can use the following command:
sudo apt-get remove kaptive-data
Uninstall kaptive-data And Its Dependencies
To uninstall kaptive-data and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove kaptive-data
Remove kaptive-data Configurations and Data
To remove kaptive-data configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge kaptive-data
Remove kaptive-data configuration, data, and all of its dependencies
We can use the following command to remove kaptive-data configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge kaptive-data
Dependencies
kaptive-data have the following dependencies:
References
Summary
In this tutorial we learn how to install kaptive-data package on Ubuntu using different package management tools: apt, apt-get and aptitude.