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

  BioPerl facilities for parsing FASTQ files using the SeqIO IO interface

• Bio::SeqAlignment

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

• 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

  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.