How to Install and Uninstall kaptive Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 20,2024

1. Install "kaptive" package

Please follow the guidelines below to install kaptive on Ubuntu 21.10 (Impish Indri)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                kaptive
            
                    
    
    Copied

2. Uninstall "kaptive" package

Please follow the guidance below to uninstall kaptive on Ubuntu 21.10 (Impish Indri):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                kaptive
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the kaptive package on Ubuntu 21.10 (Impish Indri)

Package: kaptive
Architecture: all
Version: 0.7.3-3
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 108
Depends: python3:any, python3-biopython, ncbi-blast+
Suggests: kaptive-data, kaptive-example
Filename: pool/universe/k/kaptive/kaptive_0.7.3-3_all.deb
Size: 32636
MD5sum: b4808e0222008ff85e167ac2a6fa5846
SHA1: 08230b63e1f189c41aa6f8c60c0b71d27d3b0776
SHA256: aa986c35aed4ded7a6cb8596599072e4237a9154aaef73f6c6b33bd6f04038c6
SHA512: c18bedbce102c1268d9403d6b1430dc7742b2b8ff1aeac69830bb5728f64d2c3303ba15a0e59d8faf416e6edcdf2f90023a6a91efe427576525f4e9e71c634f8
Homepage: https://github.com/katholt/Kaptive
Description-en: obtain information about K and O types for Klebsiella genome assemblies
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.
Description-md5: 96dbd0eadee18b136a9def4564674290