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Bio-SeqAlignment-0.02
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/ Bio::SeqAlignment

NAME

Bio::SeqAlignment - Aligning (and pseudo aligning) biological sequences

VERSION

version 0.02

SYNOPSIS

A collection of tools and libraries for aligning biological sequences from within Perl. External tools are available as shared and static libraries and command line tools that can be used to build Perl programs and distributions to carry out biological sequence alignment and pseudo alignment.

DESCRIPTION

The Bio::SeqAlignment distribution provides a wrapper over collection of tools, static and dynamic libraries for (pseudo-)aligning biological. sequences. The overarching aim is to provide a Perl ecosystem that can be used to build components that can be integrated in pipelines and workflows (e.g. nextflow, snakemake, etc) for sequencing experiments, or stand alone Perl applications that can utilize an extremely rich ecosystem of Perl modules and libraries for bioinformatics.

Perl had always been a very strong language for wrapping external tools, to create a seamless experience for the programmer and the emergence of the Alien namespace has made it even easier to handle dependencies on external tools and libraries. Modules that are part of the Bio::SeqAlignment distribution may be classified as:

  • External Command Line Tools

  • External Libraries

  • Components (modules) for building Perl applications

  • Perl Applications

  • Examples and Tutorials

EXTERNAL COMMAND LINE TOOLS

Command line tools that can perform sequence alignment and pseudo alignment that are made available through the Alien namespace.

  • bowtie2

    This distribution provides bowtie2 so that it can be used by other Perl distributions that are on CPAN.

  • edlib

    This distribution provides edlib so that it can be used by other Perl distributions that are on CPAN. Note that the edlib CLI is not provided for Windows.

  • hmmer3

    This distribution provides hmmer3 so that it can be used by other Perl distributions that are on CPAN.

  • last

    This distribution provides last so that it can be used by other Perl distributions that are on CPAN.

  • minimap2

    This distribution provides minimap2 so that it can be used by other Perl distributions that are on CPAN.

  • MMseqs2

    This distribution provides MMseqs2 so that it can be used by other Perl distributions that are on CPAN.

  • parasail

    This distribution provides parasail so that it can be used by other Perl distributions that are on CPAN.

EXTERNAL LIBRARIES

Alignent suite that are available as shared and static libraries for use with Inline/XS/FFI & SWIG. Those are made available through the Alien namespace.

  • edlib

    This distribution provides edlib static and shared libraries so that they can be used by other Perl distributions that are on CPAN.

  • parasail

    This distribution provides the static and dynamic libraries for parasail so that they can be used by other Perl distributions that are on CPAN.

COMPONENTS

Modules that can be used to build Perl applications for sequence alignment. Components are modules that solve a specific problem or provide a specific functionality in the context of sequence alignment. These modules utilize the external tools and libraries that are part of the Bio::SeqAlignment distribution, and may also use other Perl modules that are available on CPAN. These components can be used to build self-contained Perl applications, or they can be used in non-Perl pipelines, such as Nextflow, Snakemake, etc.

Adapter & Barcode Identification and Trimming

Modules that can assist with adapter and primer identification in sequencing data.

  • cutadapt

    This module provides an interface to the cutadapt tool for identifying and trimming adapters and primers from sequencing data.

PolyA tail trimming

Modules that can assist with polyA tail trimming in RNA-seq data.

  • cutadapt

    This module provides an interface to the cutadapt tool which can be used (among other things) to trim polyA tails from RNA-seq data.

Read Mapping

Modules that can assist with read mapping of sequencing data.

Quantitative (RNA) Sequencing

Modules that can assist with quantification of RNA-seq data.

APPLICATIONS

Perl applications that are built using the components that wrap the external tools and libraries that are part of the Bio::SeqAlignment distribution. These applications can be used as standalone tools, or they can be integrated into pipelines and workflows for sequencing experiments. The major difference between components and applications is that applications are "complete" solutions that incorporate multiple components to solve a specific problem. On the other hand, components are "building blocks" that solve a specific subtask in the context of sequence alignment. While Bio::SeqAlignment does not intend to (and in fact cannot) compete with high-performance data pipelines, the applications listed here may provide an alternative to complex workflows for simple problems e.g. in quantitative or targeted sequencing, especially for field applications with portable sequencing equipment.

EXAMPLES AND TUTORIALS

Simple examples and tutorials that demonstrate how to use external tools and libraries to build Perl applications for sequence alignment.

SEE ALSO

  • Alien

    Documentation on the Alien concept itself.

  • Alien::Base

    The base class for this Alien. The methods in that class allow you to use the static and the dynamic edlib library in your code.

  • Alien::Build::Manual::AlienUser

    Detailed manual for users of Alien classes.

  • Inline

    Write Perl Subroutines in Other Programming Languages.

  • FFI

    Perl Foreign Function Interface based on libffi. This module provides a low-level foreign function interface to Perl. It allows the calling of any function for which the user can supply an address and calling signature.

  • FFI::Platypus

    Platypus is a library for creating interfaces to machine code libraries written in languages like C, C++, Go, Fortran, Rust, Pascal. Essentially anything that gets compiled into machine code. This implementation uses libffi to accomplish this task.

  • SWIG

    SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

  • XS

    XS is an interface description file format used to create an extension interface between Perl and C code (or a C library) which one wishes to use with Perl. The XS interface is combined with the library to create a new library which can then be either dynamically loaded or statically linked into perl. The XS interface description is written in the XS language and is the core component of the Perl extension interface.

  • BioPerl

    The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science.

  • FAST

    The Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.

  • NextFlow

    Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

  • Snakemake

    The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.

AUTHOR

Christos Argyropoulos <chrisarg@gmail.com>

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.