SIMPLEX Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data 英文参考文献.docVIP

SIMPLEX:Cloud-EnabledPipelinefortheComprehensive AnalysisofExomeSequencingData MariaFischer1*,ReneSnajder1,2,StephanPabinger1,AndreasDander1,2,AnnaSchossig3, JohannesZschocke3,ZlatkoTrajanoski1,GernotStocker1* 1Division for Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria, 2Oncotyrol, Center for Personalized Cancer Medicine, Innsbruck, Austria, 3DivisionofHumanGenetics,Biocenter,InnsbruckMedicalUniversity,Innsbruck,Austria Abstract Inrecentstudies,exomesequencinghasproventobeasuccessfulscreeningtoolfortheidentificationofcandidategenes 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 developedandpublishedapplicationstoperformthefollowingsteps:(a)initialqualitycontrol,(b)intelligentdatafiltering andpre-processing,(c)sequencealignmenttoareferencegenome,(d)SNPandDIPdetection,(e)functionalannotationof variantsusingdifferentapproaches,and(f)detailedreportgenerationduringvariousstagesoftheworkflow.Thepipeline 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 researchprojectsincludingstudiestoelucidatetheroleofraregeneticdiseases.Thepipelineiscontinuouslytestedandis publiclyavailableundertheGPLasaVirtualBoxorCloudimageathttp://simplex.i-med.ac.at;additionalsupplementarydata isprovidedathttp://www.icbi.at/exome. Citation: Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, et al. (2012) SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing