How to Install and Uninstall mira-assembler Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 05,2024

1. Install "mira-assembler" package

This is a short guide on how to install mira-assembler on Ubuntu 16.04 LTS (Xenial Xerus)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                mira-assembler
            
                    
    
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2. Uninstall "mira-assembler" package

Here is a brief guide to show you how to uninstall mira-assembler on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
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                sudo apt remove
            
                        
                mira-assembler
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the mira-assembler package on Ubuntu 16.04 LTS (Xenial Xerus)

Package: mira-assembler
Priority: optional
Section: universe/science
Installed-Size: 5500
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Source: mira
Version: 4.9.5-5
Depends: libboost-filesystem1.58.0, libboost-regex1.58.0, libboost-system1.58.0, libboost-thread1.58.0, libc6 (>= 2.14), libexpat1 (>= 2.0.1), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6)
Suggests: mira-examples, mira-doc
Filename: pool/universe/m/mira/mira-assembler_4.9.5-5_amd64.deb
Size: 1796674
MD5sum: 09b097f0918463f04553f4aa277090e1
SHA1: 9cedf0cd5a59b222fdc72facbfdf98263181761b
SHA256: e150f677e01735603908310cfd57f3b589ff20147d4d7400ddfa8bee0276ef26
Description-en: Whole Genome Shotgun and EST Sequence Assembler
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
specialised on reconstructing pristine mRNA transcripts while
detecting and classifying single nucleotide polymorphisms (SNP)
occurring in different variations thereof.
.
The assembler is routinely used for such various tasks as mutation
detection in different cell types, similarity analysis of transcripts
between organisms, and pristine assembly of sequences from various
sources for oligo design in clinical microarray experiments.
.
The package provides the following executables:
Binaries provided:
* mira: for assembly of genome sequences
* miramem: estimating memory needed to assemble projects. Realised through
link to mira.
* convert_project: for converting project file types into other types
* caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
frequently used file converters (realised through links to convert_project)
* scftool: set of tools useful when working with SCF trace files
* fastatool: set of tools useful when working with FASTA trace files
.
Scripts provided:
* fasta2frag: fragmenting sequences into smaller, overlapping
subsequences. Useful for simulating shotgun sequences. Can create
subsequences in both directions (/default) and also paired-end sequences.
* fastaselect: given a FASTA file (and possibly a FASTA quality file) and
a file with names of reads, select the sequences from the input FASTA (and
quality file) and writes them to an output FASTA
* fastqselect: like fastaselect, only for FASTQ
* fixACE4consed: Consed has a bug which incapacitates it from reading
consensus tags in ACE files written by the MIRA assembler (and possibly
other programs). This script massages an ACE file so that consed can read
the consensus tags.
Description-md5: 385a6658adee0ece003867bb8ae27a2a
Homepage: http://chevreux.org/projects_mira.html
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu