群体遗传学课件：4-Variation detection based on next generation sequencing data.pdf

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1、VariationdetectionbasedonnextgenerationsequencingdataXinLIUDepartmentofScienceandTechnology,BGI2012.07.10Outline•DetectionofSNPs–Mappingshortreadsbacktothegenome;–DifferentmethodstodetectindividualSNPs;–DifferentmethodstodetectpopulationSNPs.•DetectionofInDels–Mappingwit

2、hgapsallowed;–DetectionofInDelsbySOAPindel;–OthermethodstodetectInDels•DetectionofSVs–DetectionofSVbasedoninsertsizeinformation;–DetectionofSVbasedonassembly;–DifferentmethodstodetectSVs.•DetectionofCNVs2Flowchartofre-sequencing3DifferentgenomicvariationsGenomesizeKaryot

3、ypesDNAsequencesChromosomeStructuralvariationsIndelsSNPsrearrangements4Detectionofvariations5ImportanceofSNPs•Well-studiedvariation•Betterrepresentingdemographichistory•Methodofdetectionisrelativelymature•Providesmoreinformationforfollow-upstudies•DetectSNPsinindividuals

4、•DetectSNPsinpopulation6Alignment•Findthesequencedread’splacementinreferencegenome•Calculatethecoverageanddepthdistributionofthesequencedreads•Sequencingqualityevaluation•ForSNPdetection7SOAP•Differencesbetweentraditionalandnext-generationsequencingtechnology–readslength

5、–datacapacity•Algorithmchangetomeetthedatacharacteristicsofthesequencingtechnology–traditionalaligner:globalorlocalalignment;scoringmatrix;dynamicprogrammingandtrace-back–Next-Genaligner:Indexing&Bitwiseoperation•Doesblastall/blatstillwork?•ShortOligonucleotideAlignment/

6、AnalysisPackage8AlgorithmofSOAP•ComparingtoBLAST,BLAT,shortreadsalignerappliedlooking-upmethod.•Indexofthereferenceweremadeinordertohelptheprocessoflooking-up.•Seedwerefirstlookedupbyusingindexandthensequenceswereextended.9ExampleofmappingReferenceIndexReads10FeaturesofS

7、OAP•Fastandefficient•Modeofpair-endmapping•Permitgapswithinalignments•Trimofreadspermitted11AlgorithmofSOAP2•Indexing–Splitreadintoparts,whichusedtoanchortheexactmatchingregioninthereference,excludingmuchoftheunwantedregion.•2way-BWT(Burrows-Wheelertransform)provideaexce

8、llentsolutionforthecomputingcomplexity–Memoryeffective(~7Gmemoryneedfor3Ggenome).–Fastindexing(2minutes