How to Install and Uninstall atropos Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: December 28,2024

1. Install "atropos" package

Please follow the steps below to install atropos on Ubuntu 20.10 (Groovy Gorilla)


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

Please follow the instructions below to uninstall atropos on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                atropos
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the atropos package on Ubuntu 20.10 (Groovy Gorilla)

Package: atropos
Architecture: amd64
Version: 1.1.24+dfsg-1build1
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: 912
Depends: libc6 (>= 2.4), cython3, python3 (<< 3.9), python3 (>= 3.8~), python3:any, python3-pysam
Recommends: python3-jinja2
Filename: pool/universe/a/atropos/atropos_1.1.24+dfsg-1build1_amd64.deb
Size: 219892
MD5sum: 4cbb628f7d2bda2c1891ffe8823c5dc2
SHA1: 767803b29586b2794d74293048049676828f5e23
SHA256: aecc2ddee7d56574113f7714c47e569ae684dc87fa561e76b062445ac4e23ce6
SHA512: aeaed423f98f621d14a6b712d75d412a23a4c9877553d6bbbe4578b9bb2c9a0700ea4b6f9bcf989d8a4cd8208a8ac2de8e55b9f29efa46293f2de8cc9e8a58f2
Homepage: https://github.com/jdidion/atropos
Description-en: NGS read trimming tool that is specific, sensitive, and speedy
Atropos is tool for specific, sensitive, and speedy trimming of NGS
reads. It is a fork of the venerable Cutadapt read trimmer, with the
primary improvements being:
.
1. Multi-threading support, including an extremely fast "parallel
write" mode.
2. Implementation of a new insert alignment-based trimming algorithm
for paired-end reads that is substantially more sensitive and
specific than the original Cutadapt adapter alignment-based
algorithm. This algorithm can also correct mismatches between the
overlapping portions of the reads.
3. Options for trimming specific types of data (miRNA, bisulfite-seq).
4. A new command ('detect') that will detect adapter sequences and
other potential contaminants.
5. A new command ('error') that will estimate the sequencing error
rate, which helps to select the appropriate adapter- and quality-
trimming parameter values.
6. A new command ('qc') that generates read statistics similar to
FastQC. The trim command can also compute read statistics both
before and after trimming (using the '--stats' option).
7. Improved summary reports, including support for serialization
formats (JSON, YAML, pickle), support for user-defined templates
(via the optional Jinja2 dependency), and integration with MultiQC.
8. The ability to merge overlapping reads (this is experimental and
the functionality is limited).
9. The ability to write the summary report and log messages to
separate files.
10. The ability to read SAM/BAM files and read/write interleaved
FASTQ files.
11. Direct trimming of reads from an SRA accession.
12. A progress bar, and other minor usability enhancements.
Description-md5: 6d8a51e28a71effebfff42f9cbd1e5bc