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 bran cond sub pod time code
1             package App::Sandy;
2             # ABSTRACT: App builder that simulates single-end and paired-end reads.
3              
4 1     1   3121 use App::Sandy::Base 'class';
  1         3  
  1         8  
5              
6             extends 'App::Sandy::CLI::App';
7              
8             our $VERSION = '0.22'; # 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 0.22
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             -u, --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 bioinformatic tool that provides a simple engine to generate
64             single-end/paired-end reads from a given fasta file. Many next-generation
65             sequencing analyses rely on hypothetical models and principles that are
66             not precisely satisfied in practice. Simulated data, which provides positive
67             controls, would be a perfect way to overcome these difficulties. Here, we
68             present Sandy, a straightforward, easy to use, fast, complete set of tools
69             to generate synthetic second and third-generation sequencing reads. Sandy
70             simulates whole genome sequencing, whole exome sequencing, RNAseq reads.
71             Sandy presents also several features to the users manipulate the data, as
72             well as well-organized database containing the ‘true’ information (based on
73             the generated data) of the reads position into the genome, gene and transcript
74             expression, sequencing errors, and the sequencing coverage. One of the most
75             impressive features of Sandy is the power to simulate polymorphisms as snvs,
76             indels and structural variations (e.g. gene duplication, retro-duplication,
77             gene-fusion) along with the sequencing reads - with no need of further processing
78             steps. Sandy can be used therefore for benchmarking results of a variety of
79             pipelines in the genomics or transcriptomics, as well as in generating new
80             hypotheses and helping in the best designing of sequencing projects, possibly
81             optimizing time and costs.
82              
83             =head1 AUTHORS
84              
85             =over 4
86              
87             =item *
88              
89             Thiago L. A. Miller <tmiller@mochsl.org.br>
90              
91             =item *
92              
93             J. Leonel Buzzo <lbuzzo@mochsl.org.br>
94              
95             =item *
96              
97             Felipe R. C. dos Santos <fsantos@mochsl.org.br>
98              
99             =item *
100              
101             Helena B. Conceição <hconceicao@mochsl.org.br>
102              
103             =item *
104              
105             Gabriela Guardia <gguardia@mochsl.org.br>
106              
107             =item *
108              
109             Fernanda Orpinelli <forpinelli@mochsl.org.br>
110              
111             =item *
112              
113             Pedro A. F. Galante <pgalante@mochsl.org.br>
114              
115             =back
116              
117             =head1 COPYRIGHT AND LICENSE
118              
119             This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.
120              
121             This is free software, licensed under:
122              
123             The GNU General Public License, Version 3, June 2007
124              
125             =cut