SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery 英文参考文献.docVIP

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SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery 英文参考文献.doc

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SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery 英文参考文献

SAP—ASequenceMappingandAnalyzingProgramfor LongSequenceReadsAlignmentandAccurateVariants Discovery ZhengSun,WeidongTian* StateKeyLaboratoryofGeneticEngineering,InstituteofBiostatistics,SchoolofLifeSciences,FudanUniversity,Shanghai,China Abstract The third-generation of sequencing technologies produces sequence reads of 1000bp or more that may contain high polymorphism information. However, most currently available sequence analysis tools are developed specifically for analyzingshortsequencereads.WhilethetraditionalSmith-Waterman(SW)algorithmcanbeusedtomaplongsequence reads,itsnaiveimplementationiscomputationallyinfeasible.WehavedevelopedanewSequencemappingandAnalyzing Program(SAP)thatimplementsamodifiedversionofSWtospeedupthealignmentprocess.Inbenchmarkswithsimulated and real exon sequencing data and a real E. coli genome sequence data generated by the third-generation sequencing technologies, SAP outperforms currently available tools for mapping short and long sequence reads in both speed and proportionofcapturedreads.Inaddition,itachieveshighaccuracyindetectingSNPsandInDelsinthesimulateddata.SAP isavailableat/davidsun/SAP. Citation:SunZ,TianW(2012)SAP—ASequenceMappingandAnalyzingProgramforLongSequenceReadsAlignmentandAccurateVariantsDiscovery.PLoS ONE7(8):e42887.doi:10.1371/journal.pone.0042887 Editor:HaixuTang,IndianaUniversity,UnitedStatesofAmerica ReceivedApril16,2012;AcceptedJuly12,2012;PublishedAugust7,2012 Copyright:?2012Sun,Tian.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricted use,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:TheNationalBasicResearchProgramofChina(GrantNo.2012CB316505,2010CB529505),andtheNationalNaturalScienceFoundationofChina(Grant No31071113).Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexi