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

Last updated: November 26,2024

1. Install "reapr" package

This tutorial shows how to install reapr on Ubuntu 21.10 (Impish Indri)


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

In this section, we are going to explain the necessary steps to uninstall reapr on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                reapr
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the reapr package on Ubuntu 21.10 (Impish Indri)

Package: reapr
Architecture: amd64
Version: 1.0.18+dfsg-5build1
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: 1073
Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), libtabixpp0 (>= 1.0.0), samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl
Filename: pool/universe/r/reapr/reapr_1.0.18+dfsg-5build1_amd64.deb
Size: 199612
MD5sum: 895994a0d3e258f9723242ddf189ad48
SHA1: adc68adf6fa618e6dec07e9918cb9b29db106c0f
SHA256: a738e8cddc7febfaf1cb218be4b2844d0439de28281d01b2a0a4f492be581662
SHA512: c65c3c3b2eba78a8449ef9d8e3ac75c18262c56777e12a44fd4c8daa0784f6c9c7c0ef1dcabe7757f70da9e7ec5a80c50c490a0b2f22fecbbc6c6f1cf9b4ce54
Homepage: https://www.sanger.ac.uk/science/tools/reapr
Description-en: universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped
paired end reads, without the use of a reference genome for comparison. It can
be used in any stage of an assembly pipeline to automatically break incorrect
scaffolds and flag other errors in an assembly for manual inspection. It
reports mis-assemblies and other warnings, and produces a new broken assembly
based on the error calls.
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The software requires as input an assembly in FASTA format and paired reads
mapped to the assembly in a BAM file. Mapping information such as the fragment
coverage and insert size distribution is analysed to locate mis-assemblies.
REAPR works best using mapped read pairs from a large insert library (at least
1000bp). Additionally, if a short insert Illumina library is also available,
REAPR can combine this with the large insert library in order to score each
base of the assembly.
Description-md5: 293360a33ad6e6e8a412e05853784134