How to Install and Uninstall hisat2 Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 04,2024

1. Install "hisat2" package

This is a short guide on how to install hisat2 on Ubuntu 20.10 (Groovy Gorilla)


    
        
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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 guidelines below to uninstall hisat2 on Ubuntu 20.10 (Groovy Gorilla):


    
        
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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 20.10 (Groovy Gorilla)

Package: hisat2
Architecture: amd64
Version: 2.2.1-1
Built-Using: simde (= 0.5.0-1)
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: 14161
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_2.2.1-1_amd64.deb
Size: 3654160
MD5sum: 34c749f6305c3b7df756af998b21c2a7
SHA1: 08692df6193d48501a8f22ba89bc49ee3ea15478
SHA256: ba4a03e7f35fe8f2fe0df525f6b87b276b46eef138ab1dc945c1e46ff1566252
SHA512: 14884c23555a3cb9ed433ba7bd564f931e8506e955f175e07e75ac31802dd80693a697b1705509bbff6987131b6c74fc4d6f4e8c579e27960e07499462f0ecb1
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