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

Last updated: November 22,2024

1. Install "segemehl" package

Please follow the instructions below to install segemehl on Ubuntu 21.10 (Impish Indri)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                segemehl
            
                    
    
    Copied

2. Uninstall "segemehl" package

This is a short guide on how to uninstall segemehl on Ubuntu 21.10 (Impish Indri):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                segemehl
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the segemehl package on Ubuntu 21.10 (Impish Indri)

Package: segemehl
Architecture: amd64
Version: 0.3.4-3
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 (>= 2.33), libhts3 (>= 1.10), zlib1g (>= 1:1.2.2.4)
Filename: pool/universe/s/segemehl/segemehl_0.3.4-3_amd64.deb
Size: 295796
MD5sum: 588f37ae0085f9d95aa3d734fb969397
SHA1: 86290b504cd51400548d5eb2cbed7e4985a3b816
SHA256: 11e2d6b3985b0c63240cec6762aefa83aa7e9613d32950586ef22e5a5ba90a2f
SHA512: d9dd29c0bf5816ed1d8f3ad8aaa47360082e85312670f260706e094d7a94f1018903857a2f0069164ece81d8e96abc2f0bbc8a7d59ce5ab905f93d72c09c7130
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