https://github.com/chrisarg/alien-seqalignment-cutadapt

Sequence Alignment module
https://github.com/chrisarg/alien-seqalignment-cutadapt

bioinformatics-tool polyadenylation sequencing

Last synced: 6 months ago
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Sequence Alignment module

• Host: GitHub
• URL: https://github.com/chrisarg/alien-seqalignment-cutadapt
• Owner: chrisarg
• License: other
• Created: 2024-03-04T00:36:25.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-03-24T04:08:27.000Z (over 1 year ago)
• Last Synced: 2025-03-25T11:50:20.983Z (6 months ago)
• Topics: bioinformatics-tool, polyadenylation, sequencing
• Language: Perl
• Homepage:
• Size: 52.7 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes
  • License: LICENSE

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README

          
NAME

    Alien::SeqAlignment::cutadapt - Find or install cutadapt

VERSION

    version 0.05

SYNOPSIS

    Command line tool:

     system 'cutadapt' (list of arguments and options);

     system "cutadapt  (list of argumentns and options)"; # less safe

    or you can even do this to maintain compatibility with the Alien tool

    API

     system Alien::SeqAlignment::cutadapt->cutadapt (list of arguments and options)

DESCRIPTION

    This distribution provides the python tool cutadapt so that it can be

    used by other Perl distributions that are on CPAN. It does this by first

    trying to detect an existing install of cutadapt on your system. If

    found it will use that. If it cannot be found, it will use the Python

    package installer pipx to download and install cutadapt in an isolated

    environment for each user. Note that after installation one ends up with

    a tool that can be used from the shell (i.e. no need for Perl), hence

    uninstalling the Perl module will not uninstall cutadapt or pipx. If you

    would like to uninstall cutadapt, then you should use pipx to uninstall

    it as in:

     pipx uninstall cutadapt.

    Note that the installation method of pipx varies by operating system.

    MacOS and Windows users should have working installations of homebrew

    and scoop respectively to use this Perl Alien module.

METHODS

  cutadapt

     Alien::SeqAlignment::cutadapt->cutadapt

    Returns the command name for running the CLI version of the cutadapt

    CLI.

SEE ALSO

    *   cutadapt 

        Cutadapt finds and removes adapter sequences, primers, poly-A tails

        and other types of unwanted sequence from your high-throughput

        sequencing reads.

        Cleaning your data in this way is often required: Reads from

        small-RNA sequencing contain the 3' sequencing adapter because the

        read is longer than the molecule that is sequenced. Amplicon reads

        start with a primer sequence. Poly-A tails are useful for pulling

        out RNA from your sample, but often you don't want them to be in

        your reads.

        Cutadapt helps with these trimming tasks by finding the adapter or

        primer sequences in an error-tolerant way. It can also modify and

        filter single-end and paired-end reads in various ways. Adapter

        sequences can contain IUPAC wildcard characters. Cutadapt can also

        demultiplex your reads.

    *   pipx 

        pipx is a tool to help you install and run end-user applications

        written in Python. It's roughly similar to macOS's brew,

        JavaScript's npx, and Linux's apt.

        It's closely related to pip. In fact, it uses pip, but is focused on

        installing and managing Python packages that can be run from the

        command line directly as applications.

        How is it Different from pip?

        pip is a general-purpose package installer for both libraries and

        apps with no environment isolation. pipx is made specifically for

        application installation, as it adds isolation yet still makes the

        apps available in your shell: pipx creates an isolated environment

        for each application and its associated packages.

        pipx does not ship with pip, but installing it is often an important

        part of bootstrapping your system.

    *   Homebrew 

        Homebrew installs the stuff you need that Apple (or your Linux

        system) didn't.

    *   Scoop 

        Scoop is a command-line installer for Windows that: *Eliminates

        permission popup windows *Hides GUI wizard-style installers

        *Prevents PATH pollution from installing lots of programs *Avoids

        unexpected side-effects from installing and uninstalling programs

        *Finds and installs dependencies automatically *Performs all the

        extra setup steps itself to get a working program

    *   Alien

        Documentation on the Alien concept itself.

    *   Alien::Base

        The base class for this Alien.

    *   Alien::Build::Manual::AlienUser

        Detailed manual for users of Alien classes.

    *   Bio::SeqAlignment 

        A collection of tools and libraries for aligning biological

        sequences from within Perl.

AUTHOR

    Christos Argyropoulos 

COPYRIGHT AND LICENSE

    This software is copyright (c) 2024 by Christos Argyropoulos.

    This is free software; you can redistribute it and/or modify it under

    the same terms as the Perl 5 programming language system itself.