# NAME Sandy - A straightforward and complete next-generation sequencing read simulator # VERSION version 0.23 # SYNOPSIS $ sandy ... # DESCRIPTION **SANDY** is a bioinformatics tool that provides a simple engine to simulate next-generation sequencing for genomic and transcriptomic data. Simulated data works as experimental control \- a key step to optimize NGS analysis - in comparison to hypothetical models. SANDY is a straightforward, easy-to-use, fast and highly customizable tool that generates reads requiring only a FASTA file as input. SANDY can simulate single/paired-end reads from both whole exome sequencing and RNA-seq as if produced from the most used second and third-generation sequencing platforms. SANDY’s reads can be simulated with genetic variations such as SNVs, indels and gene fusions. For customization purposes, SANDY have built-in (native) databases that can be easily extended with varying gene/transcript expression profiles, sequencing errors, sequencing coverages and genomic variations. # INSTALLATION **Sandy** was designed for Linux based distributions. If you are working with another type of operating system, such as macOS, Windows, try to use our docker image. For more details, see [docker/README.md](https://github.com/galantelab/sandy/blob/master/docker/README.md) file. ## PREREQUISITES Along with **Perl**, you must have **zlib**, **gcc** and **make** packages installed: - Debian/Ubuntu % apt-get install perl zlib1g-dev gcc make - CentOS/Fedora % yum install perl zlib gcc make - Archlinux % pacman -S perl zlib gcc make **Sandy** uses the **Comprehensive Perl Archive Network**, [CPAN](https://www.cpan.org/), 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::Sandy In some cases, you may need to pass the flag '--force' to **cpanm**: % cpanm --force App::Sandy If you concern about speed, you can avoid testing with the flag '--notest': % cpanm --notest App::Sandy For more details, see [INSTALL](https://github.com/galantelab/sandy/blob/master/INSTALL) file # ACKNOWLEDGMENTS - Coordination for the Improvement of Higher Level Personnel - [CAPES](http://www.capes.gov.br/) - Teaching and Research Institute from Sírio-Libanês Hospital - [Group of Bioinformatics](https://www.bioinfo.mochsl.org.br/) # AUTHORS - Thiago L. A. Miller - J. Leonel Buzzo - Felipe R. C. dos Santos - Helena B. Conceição - Rodrigo Barreiro - Gabriela Guardia - Fernanda Orpinelli - Pedro A. F. Galante # 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