https://github.com/chrisarg/alien-seqalignment-parasail

Sequence Alignment tool
https://github.com/chrisarg/alien-seqalignment-parasail

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing

Last synced: 5 months ago
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Sequence Alignment tool

• Host: GitHub
• URL: https://github.com/chrisarg/alien-seqalignment-parasail
• Owner: chrisarg
• License: other
• Created: 2024-03-10T03:12:11.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-03-24T05:16:20.000Z (almost 2 years ago)
• Last Synced: 2025-03-25T11:50:21.001Z (11 months ago)
• Topics: bioinformatics, bioinformatics-analysis, bioinformatics-scripts, sequence-alignment, sequencing
• Language: Perl
• Homepage:
• Size: 31.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes
  • License: LICENSE

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README

          
NAME

    Alien::SeqAlignment::parasail - find, build and install the parasail

    library

VERSION

    version 0.05

SYNOPSIS

    To execute the alignment using the command line tool:

     use Alien::parasail;

     system Alien::SeqAlignment::parasail->parasail_aligner, (list of options);

DESCRIPTION

    This distribution provides parasail so that it can be used by other Perl

    distributions that are on CPAN. The source code will be downloaded from

    the parasail github repo, and if that fails it will use the location of

    a fork but the author of this module. Contrary to other Alien modules,

    this one will not test for a prior install of the parasail library, but

    will install from source into a private share location for the use by

    other modules. This strategy will avoid overwritting prior system

    installs of the parasail library, and is guaranteed to use the latest

    version of parasail. The build provides the static and shared libraries,

    but also the CLI aligner (parasail_aligner).

METHODS

  parasail_aligner

     Alien::SeqAlignment::parasail->parasail_aligner

    Returns the command name for running the CLI version of the parasail

    aligner.

SEE ALSO

    *   parasail 

        parasail is a SIMD C (C99) library containing implementations of the

        Smith-Waterman (local), Needleman-Wunsch (global), and various

        semi-global pairwise sequence alignment algorithms. Here,

        semi-global means insertions before the start or after the end of

        either the query or target sequence are optionally not penalized.

        parasail implements most known algorithms for vectorized pairwise

        sequence alignment, including diagonal , blocked , striped , and

        prefix scan. Therefore, parasail is a reference implementation for

        these algorithms in addition to providing an implementation of the

        best-performing algorithm(s) to date on today's most advanced CPUs.

        parasail implements the above algorithms currently in three

        variants, 1) returning the alignment score and ending locations, 2)

        additionally returning alignment statistics (number of exact matches

        , number of similarities, and alignment length), and 3) functions

        that store a traceback for later retrieval as a SAM CIGAR string.

        The three variants exist because parasail is intended to be

        high-performing; calculating additional statistics or the traceback

        will perform slower than simply calculating the alignment score.

    *   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.

    *   Bio::SeqAlignment 

        A collection of tools and libraries for aligning biological

        sequences from within Perl.

AUTHOR

    Christos Argyropoulos 

COPYRIGHT AND LICENSE

    This software is copyright (c) 2023 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.