App::Sandy - App builder that simulates single-end and paired-end reads.
sandy [options] sandy help <command> sandy <command> ... Options: -h, --help brief help message -u, --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
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.
Thiago L. A. Miller <email@example.com>
J. Leonel Buzzo <firstname.lastname@example.org>
Felipe R. C. dos Santos <email@example.com>
Helena B. Conceição <firstname.lastname@example.org>
Gabriela Guardia <email@example.com>
Fernanda Orpinelli <firstname.lastname@example.org>
Pedro A. F. Galante <email@example.com>
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