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

Last updated: November 26,2024

1. Install "smalt" package

Please follow the guidance below to install smalt on Ubuntu 20.10 (Groovy Gorilla)


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

This guide covers the steps necessary to uninstall smalt on Ubuntu 20.10 (Groovy Gorilla):


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

Package: smalt
Architecture: amd64
Version: 0.7.6-9
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: 311
Depends: libbambamc0, libc6 (>= 2.29), zlib1g (>= 1:1.2.0.2)
Filename: pool/universe/s/smalt/smalt_0.7.6-9_amd64.deb
Size: 113728
MD5sum: aead9464819ec2f6790fb777541867aa
SHA1: ab28b6b00f5660147d64f2dc6b9422cc5d0da743
SHA256: e74125c02aede1bc4df27843f33deca3e7b2d6cadec09499630685eb3fe22d43
SHA512: a1d6fa38171f79d9307734ff61046244de0c63d996cc481f4582722ae62de25ab9a1f2dc63c286b5c6a8f9dc0261fe32fdb8d674462851b8eacc4d98e66954c1
Homepage: https://www.sanger.ac.uk/science/tools/smalt-0
Description-en: Sequence Mapping and Alignment Tool
SMALT efficiently aligns DNA sequencing reads with a reference genome.
Reads from a wide range of sequencing platforms, for example Illumina,
Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
paired reads.
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The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
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For each read, potentially matching segments in the reference are
identified from seed matches in the index and subsequently aligned with
the read using a banded Smith-Waterman algorithm.
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The best gapped alignments of each read is reported including a score
for the reliability of the best mapping. The user can adjust the
trade-off between sensitivity and speed by tuning the length and spacing
of the hashed words.
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A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
Description-md5: da0bc05ee32e6ad65fb07ec4330d5b6d