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

Last updated: April 29,2024

1. Install "samclip" package

This guide covers the steps necessary to install samclip on Ubuntu 21.10 (Impish Indri)


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

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


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

Package: samclip
Architecture: all
Version: 0.4.0-2
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: 172
Depends: perl:any
Filename: pool/universe/s/samclip/samclip_0.4.0-2_all.deb
Size: 19920
MD5sum: eaeb09d223d96e2422d2b7f9c6908b94
SHA1: cbc565f8e0ae8daaa7d2ebb417e6c35ed5ce08d3
SHA256: 98a56f76ac17b49ef1fa78d9df24468997fba2d2e1d3de6de3808dd351558eb5
SHA512: c592a74f5b7f626d5b308f4110e7acbe3eb68effc2193e87e7a5e432f7176f620c20c925afbdb2a3a6d1eb2e55bb47cf2f876968008fbdf5105adc397b528afa
Homepage: https://github.com/tseemann/samclip
Description-en: filter SAM file for soft and hard clipped alignments
Most short read aligners perform local alignment of reads to the
reference genome. Examples includes bwa mem, minimap2, and bowtie2
(unless in --end-to-end mode). This means the ends of the read may not
be part of the best alignment.
.
This can be caused by:
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* adapter sequences (aren't in the reference)
* poor quality bases (mismatches only make the alignment score worse)
* structural variation in your sample compared to the reference
* reads overlapping the start and end of contigs (including
circular genomes)
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Read aligners output a SAM file. Column 6 in this format stores the
CIGAR string. which describes which parts of the read aligned and which
didn't. The unaligned ends of the read can be "soft" or "hard" clipped,
denoted with S and H at each end of the CIGAR string. It is possible for
both types to be present, but that is not common. Soft and hard don't
mean anything biologically, they just refer to whether the full read
sequence is in the SAM file or not.
Description-md5: 05f5ccd9490c515b8a4bba32a37db5c8