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基于新测序技术的比对与组装算法.docx

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基于新测序技术的比对与组装算法 Abstract： Withthedevelopmentofhigh-throughputsequencingtechnologies,comparisonandassemblyalgorithmshavebecomeacrucialcomponentintheanalysisofgenomicsdata.Asaresult,avarietyofnewalgorithmshavebeendevelopedtoimprovetheaccuracy,speed,andefficiencyofthesemethods.Thispaperprovidesanoverviewofthecomparisonandassemblyalgorithmsthatarecurrentlyavailable,anddiscussestheirstrengthsandweaknesses. Introduction: High-throughputsequencingtechnologieshaverevolutionizedthefieldofgenomics,allowingforrapidandhigh-throughputsequencingoflargeamountsofDNAorRNA.However,theresultingsequencereadsareshortandfragmented,whichpresentsachallengeforaccuratelycomparingandassemblingthesesequences.Toaddressthisissue,variouscomparisonandassemblyalgorithmshavebeendevelopedovertheyearstoimprovetheaccuracy,yield,andspeedofthesemethods. ComparisonAlgorithms: Thegoalofcomparisonalgorithmsistomatchreadstoareferencegenomeortootherreadstoidentifysequencevariationsbetweenthesamplesbeingstudied.OneofthemostcommonalgorithmsusedforthispurposeistheBurrows-WheelerAlignment(BWA)thatworksbytransformingthereadsandthereferencegenomeintoanindex.Thisindexisthensearchedtoidentifythebestmatchforeachread. AnotherpopularalgorithmforcomparisonisBowtie2,whichusesasimilarapproachasBWA.However,itisknownforbeingfasterandmoreaccurate,particularlywhenitcomestohandlingreadswithindels(insertionsanddeletions).Whilethesealgorithmsareefficientandwidely-used,theyhavesomelimitationssuchasthedifficultyindetectingstructuralvariations,whichcanleadtoalossofaccuracy. AssemblyAlgorithms: Thegoalofassemblyalgorithmsistoconstructtheoriginalgenomeortranscriptomefromtheshortandfragmentedsequencereads.Therearetwomainapproachesusedinassemblyalgorithms:denovoassemblyandreferenceassembly. Denovoassemblyinvolvespiecingtogetheroverlappingsequencereadsintolongercontiguoussequencesthatcanbeusedtoreconstructtheoriginalgenomeortranscriptome.SomeexamplesofdenovoassemblyalgorithmsincludeVelvet,SPAdes,andSOAPdenovo.Thesealgorithmsworkbyfirstde