How to Install and Uninstall trim-galore Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 18,2024

1. Install "trim-galore" package

This is a short guide on how to install trim-galore on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                trim-galore
            
                    
    
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2. Uninstall "trim-galore" package

This tutorial shows how to uninstall trim-galore on Ubuntu 21.10 (Impish Indri):


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

Package: trim-galore
Architecture: all
Version: 0.6.6-1
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: 17512
Depends: perl:any, cutadapt
Recommends: fastqc
Filename: pool/universe/t/trim-galore/trim-galore_0.6.6-1_all.deb
Size: 17810528
MD5sum: 0c6c541fa0ee6d68432f2f9026c63020
SHA1: dce9231ea56007bc0d086b4a8a086aa498dce496
SHA256: 60f5fc5a281ce98b47b6178aaad6ce49b4d2eaadf0af39ecfc8bc7edbfd15215
SHA512: c453a8d07084c1a8b2ce542e7065afe8a9356eccee433b424d5d55c292258c61db7578d3cace407e7d26d9cee0537aa5bc7b3301bfb5bd5f0d452aca7b1dfc83
Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Description-en: automate quality and adapter trimming for DNA sequencing
Trim Galore! is a wrapper script to automate quality and adapter trimming
as well as quality control, with some added functionality to remove
biased methylation positions for RRBS sequence files (for directional,
non-directional (or paired-end) sequencing). It's main features are:
* For adapter trimming, Trim Galore! uses the first 13 bp of Illumina
standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends
of paired-end libraries), but accepts other adapter sequence, too
* For MspI-digested RRBS libraries, Trim Galore! performs quality and
adapter trimming in two subsequent steps. This allows it to remove
2 additional bases that contain a cytosine which was artificially
introduced in the end-repair step during the library preparation
* For any kind of FastQ file other than MspI-digested RRBS, Trim
Galore! can perform single-pass adapter- and quality trimming
* The Phred quality of basecalls and the stringency for adapter removal
can be specified individually
* Trim Galore! can remove sequences if they become too short during
the trimming process. For paired-end files Trim Galore! removes entire
sequence pairs if one (or both) of the two reads became shorter than
the set length cutoff. Reads of a read-pair that are longer than a
given threshold but for which the partner read has become too short
can optionally be written out to single-end files. This ensures that
the information of a read pair is not lost entirely if only one read
is of good quality
* Trim Galore! can trim paired-end files by 1 additional bp from the 3'
end of all reads to avoid problems with invalid alignments with Bowtie 1
* Trim Galore! accepts and produces standard or gzip compressed FastQ files
* FastQC can optionally be run on the resulting output files once
trimming has completed
Description-md5: 014a20fd57c45610fc72576da733e6ff