simplex cloud-enabled pipeline for the comprehensive analysis of exome sequencing data单纯形云计算管道的外显子组测序数据的综合分析.pdfVIP

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data 1 1,2 1 1,2 3 Maria Fischer *, Rene Snajder , Stephan Pabinger , Andreas Dander , Anna Schossig , 3 1 1 Johannes Zschocke , Zlatko Trajanoski , Gernot Stocker * 1 Division for Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria, 2 Oncotyrol, Center for Personalized Cancer Medicine, Innsbruck, Austria, 3 Division of Human Genetics, Biocenter, Innsbruck Medical University, Innsbruck, Austria Abstract 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 ei