How to Install and Uninstall kraken2 Package on Kali Linux

Last updated: May 20,2024

1. Install "kraken2" package

Please follow the steps below to install kraken2 on Kali Linux


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

This is a short guide on how to uninstall kraken2 on Kali Linux:


    
        
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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 Kali Linux

Package: kraken2
Version: 2.1.3-1
Installed-Size: 1971
Maintainer: Debian Med Packaging Team
Architecture: amd64
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6), python3, ncbi-blast+
Size: 868196
SHA256: 6bf53c46f2adc3a8e24f66f43bb151444c35f2b3baa3c3365721b9133eb086d7
SHA1: fc19c75a499b559c4ad2f38283e68df9823265a4
MD5sum: dc9df4488dae6523c2e94534ecf2a08e
Description: 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:
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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:
Homepage: https://www.ccb.jhu.edu/software/kraken2/
Section: science
Priority: optional
Filename: pool/main/k/kraken2/kraken2_2.1.3-1_amd64.deb