NAME
App::Sandy - App builder that simulates single-end and paired-end reads.
VERSION
version 0.17
SYNOPSIS
sandy [options]
sandy help <command>
sandy <command> ...
Options:
-h, --help brief help message
-M, --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
Main commands:
genome simulate genome sequencing
transcriptome simulate transcriptome sequencing
custom simulate custom sequencing
quality manage quality profile database
expression manage expression-matrix database
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>
Gabriela Guardia <gguardia@mochsl.org.br>
J. Leonel Buzzo <lbuzzo@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