SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer

Marco Beccuti; Francesca Cordero; Maddalena Arigoni; Riccardo Panero; Elvio G Amparore; Susanna Donatelli; Raffaele A Calogero

doi:10.1093/bioinformatics/btx674

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer

Bioinformatics. 2018 Mar 1;34(5):871-872. doi: 10.1093/bioinformatics/btx674.

Authors

Marco Beccuti¹, Francesca Cordero¹, Maddalena Arigoni², Riccardo Panero², Elvio G Amparore¹, Susanna Donatelli¹, Raffaele A Calogero²

Affiliations

¹ Department of Computer Sciences, University of Torino, 10124 Turin, Italy.
² Department of Molecular Biotechnology and Health Sciences, University of Torino, 10124 Turin, Italy.

Abstract

Summary: Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience.

Availability and implementation: Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html.

Contact: [email protected].

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation / methods*
Computational Biology / methods
Reproducibility of Results
Sequence Analysis, RNA / methods*
Software*