SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.

In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demand...

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Autores principales:	Maria Fischer, Rene Snajder, Stephan Pabinger, Andreas Dander, Anna Schossig, Johannes Zschocke, Zlatko Trajanoski, Gernot Stocker
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/77b7762cf71e439b853a654cf37f38eb
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spelling	oai:doaj.org-article:77b7762cf71e439b853a654cf37f38eb2021-11-18T07:10:06ZSIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.1932-620310.1371/journal.pone.0041948https://doaj.org/article/77b7762cf71e439b853a654cf37f38eb2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870267/?tool=EBIhttps://doaj.org/toc/1932-6203In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at; additional supplementary data is provided at http://www.icbi.at/exome.Maria FischerRene SnajderStephan PabingerAndreas DanderAnna SchossigJohannes ZschockeZlatko TrajanoskiGernot StockerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e41948 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maria Fischer Rene Snajder Stephan Pabinger Andreas Dander Anna Schossig Johannes Zschocke Zlatko Trajanoski Gernot Stocker SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
description	In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at; additional supplementary data is provided at http://www.icbi.at/exome.
format	article
author	Maria Fischer Rene Snajder Stephan Pabinger Andreas Dander Anna Schossig Johannes Zschocke Zlatko Trajanoski Gernot Stocker
author_facet	Maria Fischer Rene Snajder Stephan Pabinger Andreas Dander Anna Schossig Johannes Zschocke Zlatko Trajanoski Gernot Stocker
author_sort	Maria Fischer
title	SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
title_short	SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
title_full	SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
title_fullStr	SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
title_full_unstemmed	SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
title_sort	simplex: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/77b7762cf71e439b853a654cf37f38eb
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SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.

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