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

1. Install "pinfish" package

This guide covers the steps necessary to install pinfish on Ubuntu 21.10 (Impish Indri)


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

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


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

Package: pinfish
Architecture: amd64
Version: 0.1.0+ds-2
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: 8545
Depends: libc6 (>= 2.32), minimap2, racon
Filename: pool/universe/p/pinfish/pinfish_0.1.0+ds-2_amd64.deb
Size: 1362276
MD5sum: 0ad092f760f483b7aebed81f59280622
SHA1: af9f534f71aa0abe2d94c65630ac5792e18a7d33
SHA256: 1124d1c04238a188d9c93e8ecd04095af43c011003d11f4e74e6fafe4ceccef8
SHA512: 3602f3dbb4993831f99293eb454f5e5ab40386db7db238bcbc2b7c8e9149dd232b58ce16214445557408e927520370fc55851f59fc6e754dc9e9c8b2f951aa79
Homepage: https://github.com/nanoporetech/pinfish
Description-en: Collection of tools to annotate genomes using long read transcriptomics data
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.
Description-md5: e070704f0ce179f7e25e747b54785f16