File Coverage

lib/App/Sandy.pm

Criterion	Covered	Total	%
statement	3	4	75.0
branch			n/a
condition			n/a
subroutine	1	2	50.0
pod	1	1	100.0
total	5	7	71.4

line	stmt	sub	pod	time	code
1					package App::Sandy;
2					# ABSTRACT: App builder that simulates single-end and paired-end reads.
3
4	1	1		2591	use App::Sandy::Base 'class';
	1			2
	1			9
5
6					extends 'App::Sandy::CLI::App';
7
8					our $VERSION = '0.25'; # VERSION
9
10					sub command_map {
11	0	0	1		genome => 'App::Sandy::Command::Genome',
12					transcriptome => 'App::Sandy::Command::Transcriptome',
13					quality => 'App::Sandy::Command::Quality',
14					expression => 'App::Sandy::Command::Expression',
15					variation => 'App::Sandy::Command::Variation',
16					version => 'App::Sandy::Command::Version',
17					citation => 'App::Sandy::Command::Citation'
18					}
19
20					__END__
21
22					=pod
23
24					=encoding UTF-8
25
26					=head1 NAME
27
28					App::Sandy - App builder that simulates single-end and paired-end reads.
29
30					=head1 VERSION
31
32					version 0.25
33
34					=head1 SYNOPSIS
35
36					sandy [options]
37					sandy help <command>
38					sandy <command> ...
39
40					Options:
41					-h, --help brief help message
42					-H, --man full documentation
43
44					Help commands:
45					help show application or command-specific help
46					man show application or command-specific documentation
47
48					Misc commands:
49					version print the current version
50					citation export citation in BibTeX format
51
52					Database commands:
53					quality manage quality profile database
54					expression manage expression-matrix database
55					variation manage structural variation database
56
57					Main commands:
58					genome simulate genome sequencing
59					transcriptome simulate transcriptome sequencing
60
61					=head1 DESCRIPTION
62
63					B<Sandy> is a bioinformatics tool that provides a simple engine to simulate next-generation
64					sequencing for genomic and transcriptomic data. Simulated data works as experimental control
65					- a key step to optimize NGS analysis - in comparison to hypothetical models. B<Sandy> is a
66					straightforward, easy-to-use, fast and highly customizable tool that generates reads requiring
67					only a FASTA file as input. B<Sandy> can simulate single/paired-end reads from both whole exome
68					sequencing and RNA-seq as if produced from the most used second and third-generation sequencing
69					platforms. B<Sandy>’s reads can be simulated with genetic variations such as SNVs, indels and gene
70					fusions. For customization purposes, B<Sandy> have built-in (native) databases that can be easily
71					extended with varying gene/transcript expression profiles, sequencing errors, sequencing
72					coverages and genomic variations.
73
74					=head1 AUTHORS
75
76					=over 4
77
78					=item *
79
80					Thiago L. A. Miller <tmiller@mochsl.org.br>
81
82					=item *
83
84					J. Leonel Buzzo <lbuzzo@mochsl.org.br>
85
86					=item *
87
88					Felipe R. C. dos Santos <fsantos@mochsl.org.br>
89
90					=item *
91
92					Helena B. Conceição <hconceicao@mochsl.org.br>
93
94					=item *
95
96					Rodrigo Barreiro <rbarreiro@mochsl.org.br>
97
98					=item *
99
100					Gabriela Guardia <gguardia@mochsl.org.br>
101
102					=item *
103
104					Fernanda Orpinelli <forpinelli@mochsl.org.br>
105
106					=item *
107
108					Rafael Mercuri <rmercuri@mochsl.org.br>
109
110					=item *
111
112					Rodrigo Barreiro <rbarreiro@mochsl.org.br>
113
114					=item *
115
116					Pedro A. F. Galante <pgalante@mochsl.org.br>
117
118					=back
119
120					=head1 COPYRIGHT AND LICENSE
121
122					This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.
123
124					This is free software, licensed under:
125
126					The GNU General Public License, Version 3, June 2007
127
128					=cut