NAME
    Alien::SeqAlignment::minimap2 - A Perl wrapper for the minimap2 binary
    executables

SYNOPSIS
    To execute minimap2, you can use the following code: use
    Alien::SeqAlignment::minimap2; use Env qw( @PATH ); unshift @PATH,
    Alien::SeqAlignment::hmmer3->bin_dir;

      Alien::SeqAlignment::minimap2->minimap2      (list of arguments)

DESCRIPTION
    This distribution provides minimap2 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.

METHODS
  minimap2
     Alien::SeqAlignment::minimap2->minimap2            (list of arguments)

    Returns the command name for running the CLI version of the minimap2
    aligner. Minimap2 uses a single executable to build the reference index
    and align the query sequences.

SEE ALSO
    *   minimap2 <https://github.com/lh3/minimap2>

        Minimap2 is a versatile sequence alignment program that aligns DNA
        or mRNA sequences against a large reference database. Typical use
        cases include: (1) mapping PacBio or Oxford Nanopore genomic reads
        to the human genome; (2) finding overlaps between long reads with
        error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq
        or Nanopore cDNA or Direct RNA reads against a reference genome; (4)
        aligning Illumina single- or paired-end reads; (5)
        assembly-to-assembly alignment; (6) full-genome alignment between
        two closely related species with divergence below ~15%.

        For ~10kb noisy reads sequences, minimap2 is tens of times faster
        than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and
        GMAP. It is more accurate on simulated long reads and produces
        biologically meaningful alignment ready for downstream analyses. For
        >100bp Illumina short reads, minimap2 is three times as fast as
        BWA-MEM and Bowtie2, and as accurate on simulated data.

    *   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.

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.

