How to Install and Uninstall atropos Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 22,2024

1. Install "atropos" package

Please follow the guidelines below to install atropos on Ubuntu 21.10 (Impish Indri)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                atropos
            
                    
    
    Copied

2. Uninstall "atropos" package

Please follow the instructions below to uninstall atropos on Ubuntu 21.10 (Impish Indri):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                atropos
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the atropos package on Ubuntu 21.10 (Impish Indri)

Package: atropos
Architecture: amd64
Version: 1.1.29+dfsg-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: 846
Depends: libc6 (>= 2.4), cython3, python3 (<< 3.10), python3 (>= 3.9~), python3:any, python3-pysam
Recommends: python3-jinja2
Filename: pool/universe/a/atropos/atropos_1.1.29+dfsg-1_amd64.deb
Size: 193132
MD5sum: b3155e217cb80c7fcba78dfb872c90be
SHA1: 656b492cadb54a98c7baaecaf580838015d29ca6
SHA256: b484cef641530616c1a0c53698dde4db8c0244024aca7338a08ae0556a70f4ee
SHA512: c1762bf1f5a4f83ab5da82a3853c26c4c1bfd440097131798716010bc601b340804670d94500df28e4670badbe42832effd37ed1fc9523b19684e0053d62ec7d
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