/ 
App-Sandy-0.19
River stage zero No dependents
/ App::Sandy

NAME

App::Sandy - App builder that simulates single-end and paired-end reads.

VERSION

version 0.19

SYNOPSIS

sandy [options]
sandy help <command>
sandy <command> ...

Options:
 -h, --help               brief help message
 -u, --man                full documentation

Help commands:
 help                     show application or command-specific help
 man                      show application or command-specific documentation

Misc commands:
 version                  print the current version
 citation                 export citation in BibTeX format

Database commands:
 quality                  manage quality profile database
 expression               manage expression-matrix database
 variation                manage structural variation database

Main commands:
 genome                   simulate genome sequencing
 transcriptome            simulate transcriptome sequencing

DESCRIPTION

Sandy is a bioinformatic tool that provides a simple engine to generate single-end/paired-end reads from a given fasta file. Many next-generation sequencing (NGS) analyses rely on hypothetical models and principles that are not precisely satisfied in practice. Simulated data, which provides positive controls would be a perfect way to overcome these difficulties. Nevertheless, most of NGS simulators are extremely complex to use, they do not cover all kinds of the desired features needed by the users, and (some) are very slow to run in a standard computer. Here, we present Sandy, a straightforward, easy to use, fast, complete set of tools to generate synthetic next-generation sequencing reads. Sandy simulates whole genome sequencing, whole exome sequencing, RNAseq reads and it presents several features to the users manipulate the data. Sandy can be used therefore for benchmarking results of a variety of pipelines in the genomics or trancriptomics.

AUTHORS

  • Thiago L. A. Miller <tmiller@mochsl.org.br>

  • J. Leonel Buzzo <lbuzzo@mochsl.org.br>

  • Gabriela Guardia <gguardia@mochsl.org.br>

  • Fernanda Orpinelli <forpinelli@mochsl.org.br>

  • Pedro A. F. Galante <pgalante@mochsl.org.br>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007