How to Install and Uninstall samclip Package on Kali Linux

Last updated: November 22,2024

1. Install "samclip" package

This guide covers the steps necessary to install samclip on Kali Linux


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

Learn how to uninstall samclip on Kali Linux:


    
        
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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 Kali Linux

Package: samclip
Version: 0.4.0-4
Installed-Size: 172
Maintainer: Debian Med Packaging Team
Architecture: all
Depends: perl:any
Size: 20124
SHA256: d8d091bfab2ac3d3430fb7cecdc4162ba61f19bdc70f2e6df170bbce6e71e43b
SHA1: 95287f2077c044e023065132bbb268ff6ba37ed5
MD5sum: 51af01f6255128f952ef9d6fd7ff00d1
Description: 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.
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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:
Multi-Arch: foreign
Homepage: https://github.com/tseemann/samclip
Section: science
Priority: optional
Filename: pool/main/s/samclip/samclip_0.4.0-4_all.deb