Welcome to SANDY simulator!

If you’re looking for a bioinformatics tool that provides a simple engine to generate single-end/paired-end reads from a given FASTA file or expression matrix file, then SANDY is your choice!

Introduction

SANDY is a bioinformatics 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 to manipulate the data. One of the most impressive features of SANDY is the power to simulate polymorphisms as snvs, indels and structural variations along with the sequencing reads - with no need of further processing steps. SANDY can be used therefore for benchmarking results of a variety of pipelines in genomics and trancriptomics.

So, among the most killing features, we would like to highlight these:

Contents at a Glance

  1. Introduction
  2. Documentations
  3. Installation
  4. Aknowledgements
  5. Authors
  6. Citation
  7. Copyright and License

Documentations

  1. Version 0.23 - latest

  2. Version 0.22

  3. Version 0.19

  4. Version 0.18

Installation

Prerequisites

Along with Perl, the user must have zlib, gcc, make and perldoc packages installed. To install them according to your distro, use:

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.

If you are not sure, confirm the prerequisites presented and, after this, install cpanminus package manager:

	$ 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 SANDY properly

Finally install SANDY with:

	$ cpanm App::Sandy

Important: MacOS users must add an extra option to the command above, like this:

	$ cpanm --force App::Sandy

Or get Sandy in a Docker image

If the user prefer to avoid any intallation process and have Docker, you can just pull SANDY’s* image from Docker Hub with:

	$ docker pull galantelab/sandy

And will take the latest version of SANDY, ready to rock!

So, to view some instructions about how to use SANDY from a docker image, see the manual or consult the web tutorial about Sandy usage from docker.

Important: Docker has some strict default configurations for memory and CPU usage on MacOS. Users of this system can change these configurations on their behalf by accessing the Preferences menu on the Docker icon at top right corner of their desktops.

For many more details, see the INSTALL file on SANDY’s* GitHub repository.

Aknowledgements

Authors

Citation

If SANDY was somehow useful in your research, please cite it:

DOI

DOI

BibTeX entry

@misc{thiago_miller_sandy,
	author = {Thiago Miller},
	title  = {galantelab/sandy A straightforward and complete next-generation sequencing read simulator},
	month  = {may},
	year   = {2018},
	doi    = {10.5281/zenodo.1241587},
	url    = {https://doi.org/10.5281/zenodo.1241587}
}

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

So long and thanks for all the fish!

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