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

Last updated: November 22,2024

1. Install "sickle" package

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


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

This is a short guide on how to uninstall sickle on Ubuntu 20.10 (Groovy Gorilla):


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

Package: sickle
Architecture: amd64
Version: 1.33+git20150314.f3d6ae3-2
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: 53
Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)
Filename: pool/universe/s/sickle/sickle_1.33+git20150314.f3d6ae3-2_amd64.deb
Size: 18716
MD5sum: 5dd7c4a7aad1e493e1231fecf998b273
SHA1: ac3bf53cf3737f892f4d99aef4c8330366d5ffa9
SHA256: 2f2970d598f32b9cd69cbaec871585ee5fc4092d333b54cadf5e6714513ac8e2
SHA512: 62712d9a4fa0c85f8d7ec009b8cef58b5dbef53935ac14d38e9c8a2a8c1e06fd91ad4da79a0968f35710dbb746b1ee1bd9484b4d8c21e004239ca0dcea91ab72
Homepage: https://github.com/najoshi/sickle
Description-en: windowed adaptive trimming tool for FASTQ files using quality
Most modern sequencing technologies produce reads that have deteriorating
quality towards the 3'-end. Incorrectly called bases here negatively impact
assembles, mapping, and downstream bioinformatics analyses.
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Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the 3'-end
of reads. It will also discard reads based upon the length threshold. It takes
the quality values and slides a window across them whose length is 0.1 times
the length of the read. If this length is less than 1, then the window is set
to be equal to the length of the read. Otherwise, the window slides along the
quality values until the average quality in the window drops below the
threshold. At that point the algorithm determines where in the window the drop
occurs and cuts both the read and quality strings there. However, if the cut
point is less than the minimum length threshold, then the read is discarded
entirely.
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Sickle supports four types of quality values: Illumina, Solexa, Phred, and
Sanger. Note that the Solexa quality setting is an approximation (the actual
conversion is a non-linear transformation). The end approximation is close.
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Sickle also supports gzipped file inputs.
Description-md5: 669442b6169b604f66a4edae2b8390cc