基于新测序技术的比对与组装算法-豆柴文库

您所在位置：网站首页 / 基于新测序技术的比对与组装算法.docx / 文档详情

在线预览结束，喜欢就下载吧，查找使用更方便

5 金币

下载文档

/ 2

下载提示

如果您无法下载资料，请参考说明：

1、部分资料下载需要金币，请确保您的账户上有足够的金币

2、已购买过的文档，再次下载不重复扣费

3、资料包下载后请先用软件解压，在使用对应软件打开

文本预览

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