NAME
    Alien::SeqAlignment::bowtie2 - find, build and install the bowtie2 tools

VERSION
    version 0.03

SYNOPSIS
    To execute the hmmer3 set of tools, you can use the following code:

     use Alien::SeqAlignment::bowtie2;
     use Env qw( @PATH );
     unshift @PATH, Alien::SeqAlignment::bowtie2->bin_dir;
 
     Alien::SeqAlignment::bowtie2->bowtie2_build      (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_inspect    (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2            (list of arguments)
 
     Alien::SeqAlignment::bowtie2->bowtie2_build_s    (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_inspect_s  (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_align_s    (list of arguments)

     Alien::SeqAlignment::bowtie2->bowtie2_build_l    (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_inspect_l  (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_align_l    (list of arguments)

DESCRIPTION
    This distribution provides bowtie2 so that it can be used by other Perl
    distributions that are on CPAN. The source code will be downloaded from
    the github repository and installed in a private location if it is not
    already installed in your system. The bowtie2, bowtie2-build and
    bowtie2-inspect executables are actually wrapper scripts that call
    binary programs as appropriate. The wrappers shield users from having to
    distinguish between "small" (<4GB) and "large" (>4GB) index formats.
    Also, the bowtie2 (Perl!) wrapper provides some key functionality, like
    the ability to handle compressed inputs, and the functionality for --un,
    --al and related options. While the creators of bowtie2 recommend that
    one always runs the bowtie2 wrappers and not the binaries, application
    builders may want to call these functions directly when implementing
    custom workflows. Hence, this distributions exposes all functions
    provided in bowtie2

METHODS
  bowtie2
     Alien::SeqAlignment::bowtie2->bowtie2            (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_align_s    (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_align_l    (list of arguments)

    Returns the command name for running the CLI version of the bowtie2
    aligner. The method effectively runs the perl script bowtie2.pl that is
    distributed with bowtie2. The methods
    Alien::SeqAlignment::bowtie2->bowtie2_align_s and
    Alien::SeqAlignment::bowtie2->bowtie2_align_l return the binary
    executables that align against small and large index formats
    respectively.

  bowtie2_build
     Alien::SeqAlignment::bowtie2->bowtie2_build     (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_build_s   (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_build_l   (list of arguments)

    Returns the command name for the python application bowtie2-build,that
    builds the database of the reference sequences. bowtie2-build can
    generate either small or large indexes. The wrapper will decide which
    based on the length of the input genome. If the reference does not
    exceed 4 billion characters but a large index is preferred, the user can
    specify --large-index to force bowtie2-build to build a large index
    instead. The methods Alien::SeqAlignment::bowtie2->bowtie2_build_s and
    Alien::SeqAlignment::bowtie2->bowtie2_build_l return the names of the
    *binary* executables that bowtie2-build wraps over.

  bowtie2_inspect
     Alien::SeqAlignment::bowtie2->bowtie2_inspect    (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_inspect_s  (list of arguments)
     Alien::SeqAlignment::bowtie2->bowtie2_inspect_l  (list of arguments)

    bowtie2-inspect extracts information from a Bowtie index about what kind
    of index it is and what reference sequences were used to build it. This
    method provides an interface to the python wrapper function over the
    binary executables Alien::SeqAlignment::bowtie2->bowtie2_inspect_s and
    Alien::SeqAlignment::bowtie2->bowtie2_inspect_l that inspect short and
    long format indices.

SEE ALSO
    *   bowtie2 <https://bowtie-bio.sourceforge.net/index.shtml>

        Bowtie is an ultrafast, memory-efficient short read aligner. It
        aligns short DNA sequences (reads) to the human genome at a rate of
        over 25 million 35-bp reads per hour. Bowtie indexes the genome with
        a Burrows-Wheeler index to keep its memory footprint small:
        typically about 2.2 GB for the human genome (2.9 GB for paired-end).

    *   Alien

        Documentation on the Alien concept itself.

    *   Alien::Base <https://metacpan.org/pod/Alien::Base>

        The base class for this Alien. The methods in that class allow you
        to use the static and the dynamic edlib library in your code.

    *   Alien::Build::Manual::AlienUser
        <https://metacpan.org/dist/Alien-Build/view/lib/Alien/Build/Manual/A
        lienUser.pod>

        Detailed manual for users of Alien classes.

    *   Bio::SeqAlignment <https://metacpan.org/pod/Bio::SeqAlignment>

        A collection of tools and libraries for aligning biological
        sequences from within Perl.

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.

