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BioMed Research International
Volume 2015, Article ID 403497, 11 pages
http://dx.doi.org/10.1155/2015/403497
Research Article

DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation

1University of Applied Sciences and Arts of Western Switzerland, Perolles 80, 1700 Fribourg, Switzerland
2University of Würzburg, Am Hubland, 97074 Würzburg, Germany
3Phenosystems SA, 137 Rue de Tubize, 1440 Braine le Chateau, Belgium

Received 13 March 2015; Revised 10 May 2015; Accepted 18 May 2015

Academic Editor: Hong Lu

Copyright © 2015 Beat Wolf et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.