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DNAseq workflow in a diagnostic context and an example of a user friendly implementation

Please always quote using this URN: urn:nbn:de:bvb:20-opus-144527
  • 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.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.show moreshow less

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Metadaten
Author: Beat Wolf, Pierre Kuonen, Thomas Dandekar, David Atlan
URN:urn:nbn:de:bvb:20-opus-144527
Document Type:Journal article
Faculties:Fakultät für Biologie / Theodor-Boveri-Institut für Biowissenschaften
Language:English
Parent Title (English):BioMed Research International
Year of Completion:2015
Issue:403497
Source:BioMed Research International Volume 2015, Article ID 403497. DOI: 10.1155/2015/403497
DOI:https://doi.org/10.1155/2015/403497
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Tag:algorithm; alignment; database; discovery; exome; format; genome browser; mutation; next generation sequencing; variants
Release Date:2018/06/20
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung