thiagomiller/sandy repository overview

⁠NAME

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

⁠VERSION

version 0.23

⁠SYNOPSIS

$ sandy <command> ...

⁠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 file.

⁠PREREQUISITES

Along with Perl, you must have zlib, gcc and make packages installed:

• Debian/Ubuntu

    % apt-get install perl zlib1g-dev gcc make
  

  Copy

• CentOS/Fedora

    % yum install perl zlib gcc make
  

  Copy

• Archlinux

    % pacman -S perl zlib gcc make
  

  Copy

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

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 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 [email protected]⁠
• J. Leonel Buzzo [email protected]⁠
• Felipe R. C. dos Santos [email protected]⁠
• Helena B. Conceição [email protected]⁠
• Rodrigo Barreiro [email protected]⁠
• Gabriela Guardia [email protected]⁠
• Fernanda Orpinelli [email protected]⁠
• Pedro A. F. Galante [email protected]⁠

⁠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