The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.

NAME

Sandy - A straightforward and complete next-generation sequencing read simulator

VERSION

version 0.17

SYNOPSIS

 $ sandy <command> ...

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.

INSTALLATION

PREREQUISITES

Sandy uses the Comprehensive Perl Archive Network, CPAN, as its package manager, which allows a good control over all dependencies needed. If you have Perl installed, then you may have the cpan command utility. At the first run, cpan will interactively configure your environment and mirror. In doubt, just confirm the default options presented. After this, install cpanminus:

 % cpan -i App::cpanminus

App::cpanminus will provide the cpanm utility, which has the capability of install not only Sandy, but also all its dependencies recursively.

INSTALLING

Finally install Sandy:

 % cpanm App::SimulateReads

For more details, see INSTALL file

ACKNOWLEDGMENTS

I, Thiago L. A. Miller, would like to thank:

Pedro A. F. Galante - for his guidance during my doctorate
Gabriela Guardia, Helena Conceição and Fernanda Orpinelli - for the advices and testing
J. Leonel Buzzo - for the documentation
Group of Bioinformatics of Teaching and Research Institute from Sírio-Libanês Hospital

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