/ 
App-Sandy-0.25
River stage zero No dependents
/ App::Sandy

NAME

App::Sandy - App builder that simulates single-end and paired-end reads.

VERSION

version 0.25

SYNOPSIS

sandy [options]
sandy help <command>
sandy <command> ...

Options:
 -h, --help               brief help message
 -H, --man                full documentation

Help commands:
 help                     show application or command-specific help
 man                      show application or command-specific documentation

Misc commands:
 version                  print the current version
 citation                 export citation in BibTeX format

Database commands:
 quality                  manage quality profile database
 expression               manage expression-matrix database
 variation                manage structural variation database

Main commands:
 genome                   simulate genome sequencing
 transcriptome            simulate transcriptome sequencing

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.

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>

  • Rodrigo Barreiro <rbarreiro@mochsl.org.br>

  • Gabriela Guardia <gguardia@mochsl.org.br>

  • Fernanda Orpinelli <forpinelli@mochsl.org.br>

  • Rafael Mercuri <rmercuri@mochsl.org.br>

  • Rodrigo Barreiro <rbarreiro@mochsl.org.br>

  • Pedro A. F. Galante <pgalante@mochsl.org.br>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007