How to Install and Uninstall trim-galore Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 19,2024

1. Install "trim-galore" package

This guide covers the steps necessary to install trim-galore on Ubuntu 20.10 (Groovy Gorilla)


    
        
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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

In this section, we are going to explain the necessary steps to uninstall trim-galore on Ubuntu 20.10 (Groovy Gorilla):


    
        
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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 20.10 (Groovy Gorilla)

Package: trim-galore
Architecture: all
Version: 0.6.5-2
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: 17503
Depends: perl:any, cutadapt
Recommends: fastqc
Filename: pool/universe/t/trim-galore/trim-galore_0.6.5-2_all.deb
Size: 17809488
MD5sum: 885ceb3572eed3e85f4354184a9f7fbb
SHA1: acfc81ee9a15ce2fb5650640f539070fe278836d
SHA256: 173eadef1ad1e2788227ec2783a1add1dabbc44e32acef57c858bb3723b3668b
SHA512: 7fb871c7918c763685a3369fefdb0c1f71502318fd18e3d75efc71c807e83224a6286a25f9fa14f910cb83a17379654e188f2669d718ca8df9f0f4d161982e6f
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