How to Install and Uninstall pinfish Package on Kali Linux

Last updated: May 09,2024

1. Install "pinfish" package

Please follow the guidance below to install pinfish on Kali Linux


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

Please follow the guidelines below to uninstall pinfish on Kali Linux:


    
        
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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 Kali Linux

Package: pinfish
Version: 0.1.0+ds-4
Installed-Size: 7452
Maintainer: Debian Med Packaging Team
Architecture: amd64
Depends: libc6 (>= 2.34), minimap2, racon
Size: 1278560
SHA256: 7abb54db4cb0b9a202fd94c71bc5a053c1e56d3995ecad973eacf0965a87f963
SHA1: c4a09889d08125391382f13b7dd0a4e7e09700e7
MD5sum: 4cea4ae592aaf7aa8ea24f19605b893e
Description: 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:
Homepage: https://github.com/nanoporetech/pinfish
Built-Using: golang-1.21 (= 1.21.6-1), golang-github-biogo-biogo (= 1.0.4-1), golang-github-biogo-hts (= 1.4.4+dfsg1-1), golang-github-google-uuid (= 1.3.0-1)
Section: science
Priority: optional
Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-4_amd64.deb