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

Last updated: November 26,2024

1. Install "segemehl" package

In this section, we are going to explain the necessary steps to install segemehl on Ubuntu 20.10 (Groovy Gorilla)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                segemehl
            
                    
    
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2. Uninstall "segemehl" package

Please follow the steps below to uninstall segemehl on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                segemehl
            
                    
    
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            $
        

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

Package: segemehl
Architecture: amd64
Version: 0.3.4-2build1
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: 1235
Depends: libc6 (>= 2.29), libhts3 (>= 1.10), zlib1g (>= 1:1.2.2.4)
Filename: pool/universe/s/segemehl/segemehl_0.3.4-2build1_amd64.deb
Size: 298216
MD5sum: 1e470e5e47ec8db31ee482e8d33b01a9
SHA1: d72fbfc79b16dd0cf2a661df9bd2acdd4ebea24a
SHA256: 8d30b8874cd411ef4c9295cdece3e552f8431cb6eeefce49e8fc7962e516cc4c
SHA512: fc017ba2d02d3e8d61dd6f06c68541fb53a32b7eb4835423f4a72053724d087658ce863fc0bc8b89e2548748fbc3418d342e8603e55ea08325a1611078704f42
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Description-en: short read mapping with gaps
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
Description-md5: b08b0f83dc3de0c96f519821508bbd5f