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.

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.

    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.

