How to Install and Uninstall hisat2 Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 15,2024

1. Install "hisat2" package

Please follow the guidance below to install hisat2 on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                hisat2
            
                    
    
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2. Uninstall "hisat2" package

Please follow the steps below to uninstall hisat2 on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                hisat2
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the hisat2 package on Ubuntu 21.10 (Impish Indri)

Package: hisat2
Architecture: amd64
Version: 2.2.1-2
Built-Using: simde (= 0.7.2-3)
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: 14149
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), perl:any, python3
Recommends: python3-hisat2, bcftools, samtools
Filename: pool/universe/h/hisat2/hisat2_2.2.1-2_amd64.deb
Size: 3642952
MD5sum: 6147e8510e79bcb0b6cf14a7217e9bad
SHA1: b9954dfb607d1f0c4e888f0f74741ae7bbc9a030
SHA256: c416d4469d2f4176c62db47044e1da1599d4a8cc455a9f7a5b0f6317aa8566d4
SHA512: 7acc5e7381224d2ad290bd83379b9780360e81cf11c83083acb9f33d0af9ac842a2b9e7c463ad02e70bed870b2c900459a8c601f8b29e0aca0bce8b25752188d
Homepage: https://daehwankimlab.github.io/hisat2/
Description-en: graph-based alignment of short nucleotide reads to many genomes
HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as against a single reference genome). Based on an extension of BWT for graphs
a graph FM index (GFM) was designed and implementd. In addition to using
one global GFM index that represents a population of human genomes, HISAT2
uses a large set of small GFM indexes that collectively cover the whole genome
(each index representing a genomic region of 56 Kbp, with 55,000 indexes
needed to cover the human population). These small indexes (called local
indexes), combined with several alignment strategies, enable rapid and
accurate alignment of sequencing reads. This new indexing scheme is called a
Hierarchical Graph FM index (HGFM).
Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f