Welcome to Sandy simulator! ##

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 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:

Simulate reads for genome or transcriptome from any FASTA-file with a great number of options to fit your needs.
Simulate reads from transcriptomic data, based on tissue specific expression matrix files.
Simulate reads using 3rd generation sequencing (PacBio and Nanopore) quality profiles.
Simulate reads adding many kinds of genomic variations (SNPs, INDELs, Fusions an others) in a easy to use fashion.
Choose from a bulk of ready included databases for quality profiles, expression matrixes and genomic variations.
Import and record your own datasets to fit real experimental data.

Documentations

Installation

Prerequisites

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

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, 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

For more details, see the INSTALL file on Sandy’s GitHub repository.

Aknowledgements

Coordination for the Improvement of Higher Level Personnel - CAPES
Group of Bioinformatics of the 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
Felipe R. C. Santos fsantos@mochsl.org.br
Helena B. Conceição hconceicao@mochsl.org.br
Pedro A. F. Galante pgalante@mochsl.org.br

Citation

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

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}
}

Copyright and License

The GNU General Public License, Version 3, June 2007