How to Install and Uninstall kraken2 Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 18,2024

1. Install "kraken2" package

Learn how to install kraken2 on Ubuntu 20.10 (Groovy Gorilla)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                kraken2
            
                    
    
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2. Uninstall "kraken2" package

Please follow the guidelines below to uninstall kraken2 on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                kraken2
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the kraken2 package on Ubuntu 20.10 (Groovy Gorilla)

Package: kraken2
Architecture: amd64
Version: 2.0.8~beta-1build1
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: 1596
Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 5.2), ncbi-blast+
Filename: pool/universe/k/kraken2/kraken2_2.0.8~beta-1build1_amd64.deb
Size: 772508
MD5sum: fe4455210a469a850e98da2da3060a5b
SHA1: 4fe1cbc66ee7bd3e02bf6e868d783e449afde242
SHA256: ac99d1c69c2a29dbbb3b1833a931e9f434d5c4245aa14b356b926260f3786c72
SHA512: fb00c02f6e936bad651f3b29adef26b72357c9b04e80743e63a55c0ddc189aad5df301caa0b2ccff8d5135039e3609ad7dda56385274632d55ea3d5a04c9f6f7
Homepage: https://www.ccb.jhu.edu/software/kraken2/
Description-en: taxonomic classification system using exact k-mer matches
Kraken 2 is the newest version of Kraken, a taxonomic classification
system using exact k-mer matches to achieve high accuracy and fast
classification speeds. This classifier matches each k-mer within a query
sequence to the lowest common ancestor (LCA) of all genomes containing
the given k-mer. The k-mer assignments inform the classification
algorithm. [see: Kraken 1's Webpage for more details].
.
Kraken 2 provides significant improvements to Kraken 1, with faster
database build times, smaller database sizes, and faster classification
speeds. These improvements were achieved by the following updates to the
Kraken classification program:
.
1. Storage of Minimizers: Instead of storing/querying entire k-mers,
Kraken 2 stores minimizers (l-mers) of each k-mer. The length of
each l-mer must be ≤ the k-mer length. Each k-mer is treated by
Kraken 2 as if its LCA is the same as its minimizer's LCA.
2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to
store and query minimizers to improve classification accuracy.
3. Database Structure: While Kraken 1 saved an indexed and sorted list
of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash
table is a probabilistic data structure that allows for faster
queries and lower memory requirements. However, this data structure
does have a <1% chance of returning the incorrect LCA or returning
an LCA for a non-inserted minimizer. Users can compensate for this
possibility by using Kraken's confidence scoring thresholds.
4. Protein Databases: Kraken 2 allows for databases built from amino
acid sequences. When queried, Kraken 2 performs a six-frame
translated search of the query sequences against the database.
5. 16S Databases: Kraken 2 also provides support for databases not
based on NCBI's taxonomy. Currently, these include the 16S
databases: Greengenes, SILVA, and RDP.
Description-md5: 70f2ff9ad084534e552c6c2118d2a186