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

SYNOPSIS
    Command line tool:

    cutadapt (list of 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 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.

SEE ALSO
    cutadapt <https://cutadapt.readthedocs.io/en/stable/index.html>
        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 <https://pipx.pypa.io/stable/>
        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 <https://brew.sh/>
        Homebrew installs the stuff you need that Apple (or your Linux
        system) didn't.

    Scoop <https://scoop.sh/>
        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.

AUTHOR
    Christos Argyropoulos <chrisarg@gmail.com>

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.

