https://github.com/chrisarg/alien-seqalignment-bowtie2
Sequence Alignment tool
https://github.com/chrisarg/alien-seqalignment-bowtie2
bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing
Last synced: 11 months ago
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Sequence Alignment tool
- Host: GitHub
- URL: https://github.com/chrisarg/alien-seqalignment-bowtie2
- Owner: chrisarg
- License: other
- Created: 2024-03-03T14:17:40.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-24T04:17:29.000Z (almost 2 years ago)
- Last Synced: 2025-03-25T11:50:20.938Z (11 months ago)
- Topics: bioinformatics, bioinformatics-analysis, bioinformatics-scripts, sequence-alignment, sequencing
- Language: Perl
- Homepage:
- Size: 32.2 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README
- Changelog: Changes
- License: LICENSE
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README
NAME
Alien::SeqAlignment::bowtie2 - find, build and install the bowtie2 tools
VERSION
version 0.03
SYNOPSIS
To execute the hmmer3 set of tools, you can use the following code:
use Alien::SeqAlignment::bowtie2;
use Env qw( @PATH );
unshift @PATH, Alien::SeqAlignment::bowtie2->bin_dir;
Alien::SeqAlignment::bowtie2->bowtie2_build (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_inspect (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2 (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_build_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_inspect_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_align_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_build_l (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_inspect_l (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_align_l (list of arguments)
DESCRIPTION
This distribution provides bowtie2 so that it can be used by other Perl
distributions that are on CPAN. The source code will be downloaded from
the github repository and installed in a private location if it is not
already installed in your system. The bowtie2, bowtie2-build and
bowtie2-inspect executables are actually wrapper scripts that call
binary programs as appropriate. The wrappers shield users from having to
distinguish between "small" (<4GB) and "large" (>4GB) index formats.
Also, the bowtie2 (Perl!) wrapper provides some key functionality, like
the ability to handle compressed inputs, and the functionality for --un,
--al and related options. While the creators of bowtie2 recommend that
one always runs the bowtie2 wrappers and not the binaries, application
builders may want to call these functions directly when implementing
custom workflows. Hence, this distributions exposes all functions
provided in bowtie2
METHODS
bowtie2
Alien::SeqAlignment::bowtie2->bowtie2 (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_align_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_align_l (list of arguments)
Returns the command name for running the CLI version of the bowtie2
aligner. The method effectively runs the perl script bowtie2.pl that is
distributed with bowtie2. The methods
Alien::SeqAlignment::bowtie2->bowtie2_align_s and
Alien::SeqAlignment::bowtie2->bowtie2_align_l return the binary
executables that align against small and large index formats
respectively.
bowtie2_build
Alien::SeqAlignment::bowtie2->bowtie2_build (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_build_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_build_l (list of arguments)
Returns the command name for the python application bowtie2-build,that
builds the database of the reference sequences. bowtie2-build can
generate either small or large indexes. The wrapper will decide which
based on the length of the input genome. If the reference does not
exceed 4 billion characters but a large index is preferred, the user can
specify --large-index to force bowtie2-build to build a large index
instead. The methods Alien::SeqAlignment::bowtie2->bowtie2_build_s and
Alien::SeqAlignment::bowtie2->bowtie2_build_l return the names of the
*binary* executables that bowtie2-build wraps over.
bowtie2_inspect
Alien::SeqAlignment::bowtie2->bowtie2_inspect (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_inspect_s (list of arguments)
Alien::SeqAlignment::bowtie2->bowtie2_inspect_l (list of arguments)
bowtie2-inspect extracts information from a Bowtie index about what kind
of index it is and what reference sequences were used to build it. This
method provides an interface to the python wrapper function over the
binary executables Alien::SeqAlignment::bowtie2->bowtie2_inspect_s and
Alien::SeqAlignment::bowtie2->bowtie2_inspect_l that inspect short and
long format indices.
SEE ALSO
* bowtie2
Bowtie is an ultrafast, memory-efficient short read aligner. It
aligns short DNA sequences (reads) to the human genome at a rate of
over 25 million 35-bp reads per hour. Bowtie indexes the genome with
a Burrows-Wheeler index to keep its memory footprint small:
typically about 2.2 GB for the human genome (2.9 GB for paired-end).
* 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.
* Bio::SeqAlignment
A collection of tools and libraries for aligning biological
sequences from within Perl.
AUTHOR
Christos Argyropoulos
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.