NAME

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

VERSION

version 0.20

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 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. Here, we present Sandy, a straightforward, easy to use, fast, complete set of tools to generate synthetic second and third-generation sequencing reads. Sandy simulates whole genome sequencing, whole exome sequencing, RNAseq reads. Sandy presents also several features to the users manipulate the data, as well as well-organized database containing the ‘true’ information (based on the generated data) of the reads position into the genome, gene and transcript expression, sequencing errors, and the sequencing coverage. One of the most impressive features of Sandy is the power to simulate polymorphisms as snvs, indels and structural variations (e.g. gene duplication, retro-duplication, gene-fusion) 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 the genomics or transcriptomics, as well as in generating new hypotheses and helping in the best designing of sequencing projects, possibly optimizing time and costs.

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 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, 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

For more details, see INSTALL file

ACKNOWLEDGMENTS

Coordination for the Improvement of Higher Level Personnel - CAPES
Teaching and Research Institute from Sírio-Libanês Hospital - Group of Bioinformatics

AUTHORS

  • Thiago L. A. Miller <tmiller@mochsl.org.br>

  • J. Leonel Buzzo <lbuzzo@mochsl.org.br>

  • Felipe R. C. dos Santos <fsantos@mochsl.org.br>

  • Helena B. Conceição <hconceicao@mochsl.org.br>

  • Gabriela Guardia <gguardia@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