# 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.
