NAME
    Task::FASTQTools

VERSION
    version 0.03

SYNOPSIS
    Facilities to process FASTQ files as returned from sequencing
    instruments. Convert from FASTQ to FASTA, tabular and BioX::Seq formats.

DESCRIPTION
    A collection of tools to convert, filter and analyze FASTQ/A files. This
    is mostly a playpen for me to experiment with the BioX::Seq and other
    biological sequence modules in Perl. Code may eventually find itself in
    the Bio::Seq::Alignment modules

NAME
    Task::FASTQTools- manipulate FASTQ files from perl

SUBROUTINES
  fa2BioXSeq ($input_file, $bioseq_objects_ref)
    Convert a FASTA file to an array ref of BioX::Seq objects and append
    them to the array ref that has been provided by the caller.

  fa2tab ($input_file, $output_file)
    Convert a FASTA file to tab delimited file

  fastq2a ($input_file, $output_file)
    Converts a FASTQ file to the equivalent FASTA file

  fq2BioXSeq ($input_file, $bioseq_objects_ref)
    Convert a FASTQ file to an array ref of BioX::Seq objects and append
    them to the array ref that has been provided by the caller.

  fq2tab ($input_file, $output_file)
    Convert a FASTQ file to tab delimited file

SEE ALSO
    *   BioPerl FASTQ <https://metacpan.org/pod/Bio::SeqIO::fastq>

        BioPerl facilities for parsing FASTQ files using the SeqIO IO
        interface

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

        A collection of tools and libraries for mapping biological sequences
        from within Perl using (pseudo) alignment methods.

    *   BioX::Seq <https://metacpan.org/pod/BioX::Seq>

        BioX::Seq is a simple sequence class that can be used to represent
        biological sequences. It was designed as a compromise between using
        simple strings and hashes to hold sequences and using the rather
        bloated objects of Bioperl. Benchmarking by the author of the
        present module, shows that its performance for sequence IO under the
        fast mode is nearly x2 the speed of the BioPerl SeqIO modules and
        1.5x the speed of the FAST modules. The speed is rather comparable
        to the Biopython SeqIO module.

    *   FAST <https://metacpan.org/pod/FAST>

        FAST is a collection of modules that provide a simple and fast
        interface to sequence data. It is designed to be lightweight and
        fast and it is somewhat faster than BioPerl itself.

AUTHOR
    Christos Argyropoulos <chrisarg@cpan.org>

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.

AUTHOR
    Christos Argyropoulos <chrisarg@gmail.com>

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.

