How to Install and Uninstall kaptive Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: June 02,2024

1. Install "kaptive" package

Please follow the guidance below to install kaptive on Ubuntu 20.10 (Groovy Gorilla)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                kaptive
            
                    
    
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2. Uninstall "kaptive" package

This tutorial shows how to uninstall kaptive on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                kaptive
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the kaptive package on Ubuntu 20.10 (Groovy Gorilla)

Package: kaptive
Architecture: all
Version: 0.7.0-2
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: 106
Depends: python3:any, python3-biopython, ncbi-blast+
Suggests: kaptive-data, kaptive-example
Filename: pool/universe/k/kaptive/kaptive_0.7.0-2_all.deb
Size: 30660
MD5sum: 186b1e6da95d4d6dfbf5816ac2816011
SHA1: e7bc3c63a86a70bb9fde5b7ed987a3c9c3894075
SHA256: 659f1b97d13d4a6ca21371bef7664bf42a1c2d2b74ac87299a796c6a895db47d
SHA512: 2c4f795585cfa60cdbebea00a4fda1a4830543ffb59ade33b37c083c3ffa3c65eea5bb038a68b2a66d0d750792715e4abc60bfd60cddb5518a291bebcadfebdd
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.
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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:
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* 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.
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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