CPAN::Groonga

  use strict;
  use warnings;
  package Bio::SeqAlignment::Components::Sundry;
$Bio::SeqAlignment::Components::Sundry::VERSION = '0.01';
  # ABSTRACT: Miscellaneous components for building awesome sequencing apps.
  
  1;
=head1 NAME

Bio::SeqAlignment::Components::Sundry Placeholder for miscellaneous components

=head1 VERSION

version 0.01

=head1 SYNOPSIS

  use Bio::SeqAlignment::Components::Sundry::ComponentName;


=head1 DESCRIPTION

This module reserves the name space for miscellaneous components that are 
relevant for building awesome sequencing applications using the
Bio::SeqAlignment framework. The module itself does not provide any
functionality, so you will have to load the specific components you need
as you build your application, e.g.:

  use Bio::SeqAlignment::Components::Sundry::ComponentName;

where ComponentName is the name of the component you need.

=head1 COMPONENTS

=over 4

=item B<Tailing>

This module provides functions to add various tails to the 3' of biological
sequences. Such modifications are useful for e.g. simulating polyA tails 
in RNAseq, adding UMI tags to sequences, etc.

=item B<DocumentSequenceModifications>

This module provides functions to store and retrieve sequence modifications in
various formats. These modifications provide a meta-data layer to fasta files
(and down the road to fastq files) that can be used to track changes made to
the sequences in the file. While there are many ways to store such information,
this module provides a simple way to store and retrieve it in common serialization
formats (e.g. JSON/YAML/MessagePack). Storing this information in this manner
allows for easy retrieval and use in downstream analyses and avoids the use of
the rather heavyweight BioPerl modules.

=item B<IOHelpers>

This module provides helper functions for reading and writing (simple) sequence
files. By simple sequence files, we mean files that contain only sequence data, 
such as FASTA (and some time in the future FASTQ) files. The module uses the 
BioX::Seq module to parse sequences. This is a simple module that provides a
lightweight object-oriented interface to sequence data. It is also wickedly fast.

=back

=head1 AUTHOR

Christos Argyropoulos <chrisarg@cpan.org>

=head1 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.

=cut