NAME

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

VERSION

version 0.02

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;

Then you can call the program as:

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

  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

  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

  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 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.