Complete Guide: Installing pinfish-examples on Ubuntu 21.10 (Impish Indri) 2024

1. Install "pinfish-examples" package

This guide let you learn how to install pinfish-examples on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                pinfish-examples
            
                    
    
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2. Uninstall "pinfish-examples" package

Please follow the steps below to uninstall pinfish-examples on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                pinfish-examples
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the pinfish-examples package on Ubuntu 21.10 (Impish Indri)

Package: pinfish-examples
Architecture: all
Version: 0.1.0+ds-2
Priority: optional
Section: universe/science
Source: pinfish
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 175793
Filename: pool/universe/p/pinfish/pinfish-examples_0.1.0+ds-2_all.deb
Size: 179336504
MD5sum: 47f45bb9e7c092091d171cf8f71cab39
SHA1: 57d63c18db01611c5c7f4dfad000738ec1326e1e
SHA256: 2ab86840338ed7112c6185dcdddb6334f634963b238723df5688f100e13e5f3e
SHA512: 877bf353d6858635fad76cc0c54f8f1a55c260f4bd36c635ba7552e8d6ea81a188d8b618f55da2a7ffaf50faa37cb355aecd821b2721234f9a879c9dd61f080a
Homepage: https://github.com/nanoporetech/pinfish
Description-en: Examples and test data for pinfish
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
.
This package contains a test data set as well as sample scripts
running some test suite provided by Debian also as autopkgtest.
Description-md5: 8eae3bcd591f8fbbebc4c6f807a136ec